1. technology and computing

Agilent
7200 Accurate-Mass
Quadrupole
Time-of-Flight GC/MS
System
Operation Manual
Agilent Technologies
Notices
© Agilent Technologies, Inc. 2012, 2014
Warranty
No part of this manual may be reproduced in
any form or by any means (including electronic storage and retrieval or translation
into a foreign language) without prior agreement and written consent from Agilent
Technologies, Inc. as governed by United
States and international copyright laws.
The material contained in this document is provided “as is,” and is subject to being changed, without notice,
in future editions. Further, to the maximum extent permitted by applicable
law, Agilent disclaims all warranties,
either express or implied, with regard
to this manual and any information
contained herein, including but not
limited to the implied warranties of
merchantability and fitness for a particular purpose. Agilent shall not be
liable for errors or for incidental or
consequential damages in connection with the furnishing, use, or performance of this document or of any
information contained herein. Should
Agilent and the user have a separate
written agreement with warranty
terms covering the material in this
document that conflict with these
terms, the warranty terms in the separate agreement shall control.
Manual Part Number
G3850-90008
Edition
First Edition, August 2014
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Blvd. 
Santa Clara, CA 95051
Technology Licenses
The hardware and/or software described in
this document are furnished under a license
and may be used or copied only in accordance with the terms of such license.
Restricted Rights Legend
U.S. Government Restricted Rights. Software and technical data rights granted to
the federal government include only those
rights customarily provided to end user customers. Agilent provides this customary
commercial license in Software and
technical data pursuant to FAR 12.211
(Technical Data) and 12.212 (Computer Software) and, for the Department of Defense,
DFARS 252.227-7015 (Technical Data -Commercial Items) and DFARS 227.7202-3
(Rights in Commercial Computer Software
or Computer Software Documentation).
Safety Notices
CAUTION
A CAUTION notice denotes a hazard. It calls attention to an operating procedure, practice, or the like
that, if not correctly performed or
adhered to, could result in damage
to the product or loss of important
data. Do not proceed beyond a
CAUTION notice until the indicated
conditions are fully understood and
met.
WA R N I N G
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly performed or adhered to, could result
in personal injury or death. Do not
proceed beyond a WARNING
notice until the indicated conditions are fully understood and
met.
Operation Manual
1
About This Manual
This manual contains information for operating and maintaining the Agilent
7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS system.
1
“Introduction”
Chapter 1 describes general information about the 7200 Q-TOF GC/MS,
including a hardware description, and general safety warnings.
2
“Installing GC Columns”
Chapter 2 shows you how to prepare a capillary column for use with the MS,
install it in the GC oven, and connect it to the MS using the GC/MS interface.
3
“Operating in Electron Impact (EI) Mode”
Chapter 3 describes routine operations in EI mode such as setting
temperatures, monitoring pressures, tuning, venting, and pumpdown.
4
“Operating in Chemical Ionization (CI) Mode”
Chapter 4 describes additional tasks necessary to operate in CI mode.
5
“Using the Removable Ion Source”
Chapter 5 shows you how to change the removable ion source.
6
“General Maintenance”
Chapter 6 describes general maintenance procedures for the 7200 Q-TOF
GC/MS.
Operation Manual
3
1
Hardware User Information
Accompanying your hardware and software is a comprehensive collection of
manuals, videos, user applications, and method development tools. These are
located on the:
• Agilent GC and GC/MS User Manuals and Tools DVD set
• Agilent GC/MS Software Information and Manuals memory stick
To Install Your Hardware Library
Insert Disk 1 into your DVD drive and follow the prompts.
Agilent Technologies
GC/GCMS Hardware User Manuals and Videos
Version B.01.05
Disk 2/3
Agilent Technologies
January, 2013
GC/GCMS Hardware User
To install: Manuals and Videos
Version B.01.05
January, 2013
1. Insert disk into DVD drive
2. Follow the instructions on the screen.
3. If autoplay is not enabled, double-click
"index_xx.html" on the DVD
where xx is:
en for English
ch for 中文
jp for 日本語
To install:
1. Insert disk into DVD drive
2. Follow the instructions on the screen.
© 2013 Agilent Technologies, Inc.3. If autoplay is not enabled, double-click
All rights reserved.
"index_xx.html" on the DVD
where xx is:
Made in USA
en for English
ch for 中文
jp for 日本語
Disk 2/3
S1
© 2013 Agilent Technologies, Inc.
All rights reserved.
Made in USA
S1
This can be installed by anyone who has authority to copy
information onto the receiving computer.
To Install Your Software Library
Insert the memory stick into a USB port and follow the prompts.
This can be installed by anyone who has authority to copy
information onto the receiving computer.
See the Agilent 7200 Accurate Mass Q-TOF GC/MS System Quick Start
document (G6845-90014) for more details on how to install this information
on your computer.
4
Operation Manual
1
Contents
1
Introduction
Abbreviations Used
10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Hardware Description
14
Important Safety Warnings
15
Safety and Regulatory Certifications
Intended Use
21
21
Moving or Storing the MS
2
18
21
Cleaning/Recycling the Product
Liquid Spills
21
Installing GC Columns
Columns
24
To Install a Capillary Column in a Split/Splitless Inlet
To Condition a Capillary Column
33
Operating in Electron Impact (EI) Mode
Operating the MS from the Data System
The GC/MS Interface
Pumping Down
38
39
Before You Turn On the MS
41
42
Controlling Temperatures
42
Controlling Column Flow
42
Controlling Collision Cell Flow
Operation Manual
27
31
To Install a Capillary Column in the GC/MS Interface
3
12
43
5
1
Venting the MS
44
Typical Vacuum Pressures in EI Mode
45
To Set Monitors for Temperature and Vacuum Status
To Set the MS Analyzer Temperature
46
48
To Set the GC/MS Interface Temperature from the MassHunter Workstation
To Calibrate the Column
51
To Configure the Collision Cell Gas
53
To Set the Collision Cell Gas Flow Rate
To Autotune the MS for EI Mode
55
To Remove the Upper RIS Cover
57
54
To Open the Analyzer Cover for Access to the Analyzer Sideplate
To Pump Down the MS
To Vent the MS
4
58
59
62
Operating in Chemical Ionization (CI) Mode
Setting Up Your MS to Operate in CI Mode
The GC/MS Interface
Operating the CI MS
Other Reagent Gases
CI Autotune
64
65
67
High Vacuum Pressure in CI Mode
68
70
72
The Flow Control Module
73
To Switch from the EI Mode to CI Mode
74
To Operate the Reagent Gas Flow Control Module
To Set a Reagent Gas Flow
To Perform a CI Autotune
6
50
76
78
79
Operation Manual
1
5
Using the Removable Ion Source
The Removable Ion Source
82
To Change the Ion Source
84
To Install the RIS Probe Extraction Tool
87
To Remove the Source from the Analyzer Chamber
89
To Change the Ion Source on the RIS Probe Extraction Tool
To Install the Ion Source in the Analyzer Chamber
93
To Remove the RIS Probe Extraction Tool from the Instrument
6
94
General Maintenance
Before Starting
96
Maintaining the Vacuum System
Maintaining the Analyzer
100
101
To Disassemble the EI Ion Source
To Assemble the EI Ion Source
To Disassemble the CI Ion Source
To Assemble the CI Ion Source
To Clean the Ion Source
To Remove a Filament
To Install a Filament
Operation Manual
91
103
105
108
110
112
116
118
7
1
8
Operation Manual
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
1
Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight
GC/MS System 12
Hardware Description 14
Important Safety Warnings 15
Safety and Regulatory Certifications 18
Intended Use 21
Cleaning/Recycling the Product 21
Liquid Spills 21
Moving or Storing the MS 21
This section provides general information about the 7200
Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS
System, including a hardware description, and general safety
warnings.
Agilent Technologies
9
1
Introduction
Abbreviations Used
Abbreviations Used
The abbreviations in Table 1 are used in discussing this
product. They are collected here for convenience.
Table 1
10
Abbreviations
Abbreviation
Definition
AC
Alternating current
ALS
Automatic liquid sampler
BFB
Bromofluorobenzene (calibrant)
CC
Collision cell
CI
Chemical ionization
DC
Direct current
DFTPP
Decafluorotriphenylphosphine (calibrant)
EI
Electron impact
EPC
Electronic pneumatic control
eV
Electron volt
GC
Gas chromatograph
id
Inside diameter
LAN
Local Area Network
m/z
Mass to charge ratio
MFC
Mass flow controller
MS
Mass spectrometer
NCI
Negative chemical ionization
OFN
Octafluoronaphthalene (sample)
PCI
Positive chemical ionization
PFDTD
Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)
PFET
2,4,6-tris (Pentafluoroethyl)-1,3,5-triazine
Operation Manual
Introduction
Abbreviations Used
Table 1
Operation Manual
1
Abbreviations (continued)
Abbreviation
Definition
PFTBA
Perfluorotributylamine (calibrant)
Q-TOF
Quadrupole time-of-flight
Quad
Quadrupole mass filter
RF
Radio frequency
RFPA
Radio frequency power amplifier
TOF
Time-of-flight
Torr
Unit of pressure, 1 mm Hg
Turbo
Turbomolecular vacuum pump
11
1
Introduction
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
The 7200 Accurate-Mass Quadrupole Time-of-Flight (Q-TOF)
GC/MS System is a standalone capillary GC detector for use
with the Agilent 7890 Series gas chromatograph. The 7200
Q-TOF features:
• Three turbomolecular vacuum pumps
• Rotary vane foreline pump
• Independently MS-heated EI or CI ion source
• Removable ion source (RIS) probe with RIS bayonet and
cooling chamber, which allows quick change from EI to CI ion
source with minimal loss of vacuum in the instrument
• Independently MS-heated hyperbolic quadrupole mass filter,
which can be heated to high temperatures, minimizing the
contamination typical with low temperature analyses
• Single hexapole collision cell
• Ion-focusing slicer
• Vacuum-insulated flight tube with dual-stage ion mirror
• Fast electronics, allowing fast sampling rates
• Analog to digital detector
• Independently GC-heated GC/MS interface with automatic
retraction during ion source removal
Physical description
The 7200 Q-TOF GC/MS is approximately 48 cm high, 71 cm
wide, and 89 cm deep excluding the flight tube and RIS handle.
The flight tube extends 84 cm up over the top of the instrument.
The RIS handle, when attached, extends 48 cm from the front of
the instrument.
The weight of the instrument is 152 kg for the mainframe. The
attached foreline (roughing) pump weighs an additional 21.5 kg.
12
Operation Manual
Introduction
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
1
The basic components of the instrument are: the frame/cover
assemblies, the vacuum system, the GC/MS interface, the
removable ion source, the flight tube electronics, the
quadrupole mass filter, the collision cell, and the detector.
Vacuum gauge
The 7200 Q-TOF GC/MS is equipped with four ion vacuum
gauges. The MassHunter Workstation can be used to read the
pressure (high vacuum) in the vacuum manifold, the
turbomolecular vacuum pump discharge, and the flight tube.
Ionization modes
The G3851BA 7200 Accurate-Mass Q-TOF GC/MS comes
standard with both an EI source and a CI source.
For the CI system, a methane/isobutane gas purifier is provided
and is required. It removes oxygen, water, hydrocarbons, and
sulfur compounds.
The MS CI system has been optimized to achieve the relatively
high ion source pressure required for CI while still maintaining
high vacuum in the collision cell, quadrupole, and TOF tube.
Special seals along the flow path of the reagent gas and very
small openings in the ion source keep the ion source gases in
the ionization volume long enough for the appropriate reactions
to occur. The interface has special plumbing for reagent gas. A
retractable insulating seal fits onto the tip of the interface and
is used for both CI and EI.
Switching back and forth between CI and EI ion sources takes
less than 30 minutes with the new removable ion source (RIS).
The RIS allows the instrument to remain under vacuum, and
provides a cooling chamber with N2 purge for rapid ion source
cooling without venting the machine. This saves hours in cycle
time over the traditional unit.
Operation Manual
13
1
Introduction
Hardware Description
Hardware Description
Figure 1 is an overview of a typical Agilent 7200 Accurate-Mass
Q-TOF GC/MS system.
Flight tube
ALS
7890 GC
Q-TOF
MS power
switch
Figure 1
14
Lower RIS
cover
Upper RIS
cover
GC power
switch
Tray
Oven door
latch
7200 Q-TOF GC/MS System
Operation Manual
Introduction
Important Safety Warnings
1
Important Safety Warnings
There are several important safety notices to always keep in
mind when using the instrument.
Many internal parts of these instruments carry dangerous voltages
If the instrument is connected to a power source, even if the
power switch is off, potentially dangerous voltages exist on:
• The wiring between the instrument power cord and the AC
power supply
• The AC power supply itself
• The wiring from the AC power supply to the power switch
With the power switch on, potentially dangerous voltages also
exist on:
• All electronics boards in the instrument
• The internal wires and cables connected to these boards
• The wires for any heater (oven, detector, inlet, or valve box)
WA R N I N G
All these parts are shielded by covers. With the covers in place, it should be
difficult to accidentally make contact with dangerous voltages. Unless
specifically instructed to, never remove a cover unless the detector, inlet, and
oven are turned off.
WA R N I N G
If the power cord insulation is frayed or worn, the cord must be replaced. Contact
your Agilent service representative.
Electrostatic discharge is a threat to instrument electronics
The printed circuit boards in these instruments can be damaged
by electrostatic discharge. Do not touch any of the boards
unless it is absolutely necessary. If you must handle them, wear
a grounded wrist strap and take other antistatic precautions.
Operation Manual
15
1
Introduction
Important Safety Warnings
Precautions to take to prevent an explosion
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
WA R N I N G
You MUST make sure the top thumbscrew on the front analyzer side plate and the top
thumbscrew on the rear analyzer side plate are both fastened finger-tight. Do not
over-tighten the thumbscrews; this can cause air leaks.
You MUST leave the collision cell chamber top plate shipping brackets fastened. Do
not remove the shipping brackets from the top plate for normal operation; they
secure the top plate in the event of an explosion.
WA R N I N G
Failure to secure your MS as described above greatly increases the chance of
personal injury in the event of an explosion.
Many parts are dangerously hot
Many parts of these instruments operate at temperatures high
enough to cause serious burns. These parts include, but are not
limited to the:
• Inlet
• Oven and its contents
• Valve box
• Column nuts attaching the column to an inlet, detector, or
MS interface
• Foreline pump
• GC/MS transfer line
Always cool these areas of the system to room temperature
before working on them. They will cool faster if you first set the
temperature of the heated zone to room temperature. Turn the
zone off after it has reached the setpoint. If you must perform
16
Operation Manual
Introduction
Important Safety Warnings
1
maintenance on hot parts, use a wrench and wear gloves.
Whenever possible, cool the part of the instrument that you will
be maintaining before you begin working on it.
WA R N I N G
Be careful when working behind the instrument. During cooldown cycles, the GC
emits hot exhaust that can cause burns.
WA R N I N G
The foreline pump can cause burns if touched when operating.
WA R N I N G
The insulation around the inlets, detectors, valve box, and the insulation cups is
made of refractory ceramic fibers. To avoid inhaling fiber particles, we
recommend the following safety procedures: ventilate your work area; wear long
sleeves, gloves, safety glasses, and a disposable dust/mist respirator; dispose of
insulation in a sealed plastic bag in accordance with local regulations; wash
your hands with mild soap and cold water after handling the insulation.
The oil pan under the standard foreline pump can be a fire hazard
Oily rags, paper towels, and similar absorbents in the oil pan
could ignite and damage the pump and other parts of the MS.
WA R N I N G
Operation Manual
Combustible materials (or flammable/nonflammable wicking material) placed
under, over, or around the foreline (roughing) pump constitutes a fire hazard.
Keep the pan clean, but do not leave absorbent material such as paper towels in
it.
17
1
Introduction
Safety and Regulatory Certifications
Safety and Regulatory Certifications
The 7200 Q-TOF GC/MS conforms to the following safety
standards:
• Canadian Standards Association (CSA): CAN/CSA-C22.2 No.
61010-1-04
• CSA/Nationally Recognized Test Laboratory (NRTL):
UL 61010–1
• International Electrotechnical Commission (IEC): 61010–1
• EuroNorm (EN): 61010–1
The 7200 Q-TOF GC/MS conforms to the following regulations
on Electromagnetic Compatibility (EMC) and Radio Frequency
Interference (RFI):
• CISPR 11/EN 55011: Group 1, Class A
• IEC/EN 61326-1
• AUS/NZ
This ISM device complies with Canadian ICES-001. Cet appareil
ISM est conforme a la norme NMB—001 du Canada.
The 7200 Q-TOF GC/MS is designed and manufactured under a
quality system registered to ISO 9001.
Information
The Agilent Technologies 7200 Accurate-Mass Q-TOF GC/MS
meets the following IEC (International Electrotechnical
Commission) classifications: Equipment Class I, Laboratory
Equipment, Installation Category II, and Pollution Degree 2.
This unit has been designed and tested in accordance with
recognized safety standards and is designed for use indoors. If
the instrument is used in a manner not specified by the
manufacturer, the protection provided by the instrument may
be impaired. Whenever the safety protection of the MS has been
compromised, disconnect the unit from all power sources and
secure the unit against unintended operation.
18
Operation Manual
Introduction
Safety and Regulatory Certifications
1
Refer servicing to qualified service personnel. Substituting
parts or performing any unauthorized modification to the
instrument may result in a safety hazard.
Symbols
Warnings in the manual or on the instrument must be observed
during all phases of operation, service, and repair of this
instrument. Failure to comply with these precautions violates
safety standards of design and the intended use of the
instrument. Agilent Technologies assumes no liability for the
customer’s failure to comply with these requirements.
See accompanying instructions for more information.
Indicates a hot surface.
Indicates hazardous voltages.
Indicates earth (ground) terminal.
Indicates potential explosion hazard.
Indicates radioactivity hazard.
Indicates electrostatic discharge hazard.
Indicates that you must not discard this electrical/electronic
product in domestic household waste.
Operation Manual
19
1
Introduction
Safety and Regulatory Certifications
Electromagnetic compatibility
This device complies with the requirements of CISPR 11.
Operation is subject to the following two conditions:
• This device may not cause harmful interference.
• This device must accept any interference received, including
interference that may cause undesired operation.
If this equipment does cause harmful interference to radio or
television reception, which can be determined by turning the
equipment off and on, the user is encouraged to try one or more
of the following measures:
1
Relocate the radio or antenna.
2
Move the device away from the radio or television.
3
Plug the device into a different electrical outlet, so that the
device and the radio or television are on separate electrical
circuits.
4
Make sure that all peripheral devices are also certified.
5
Make sure that appropriate cables are used to connect the
device to peripheral equipment.
6
Consult your equipment dealer, Agilent Technologies, or an
experienced technician for assistance.
Changes or modifications not expressly approved by Agilent
Technologies could void the user’s authority to operate the
equipment.
Sound emission declaration
Sound pressure
Sound pressure Lp < 70 dB according to EN 27779:1991 and 
EN ISO 3744:1995.
Schalldruckpegel
Schalldruckpegel LP < 70 dB nach EN 27779:1991 und EN ISO
3744:1995.
20
Operation Manual
Introduction
Intended Use
1
Intended Use
Agilent products must only be used in the manner described in
the Agilent product user guides. Any other use may result in
damage to the product or personal injury. Agilent is not
responsible for any damages caused, in whole or in part, by
improper use of the products, unauthorized alterations,
adjustments or modifications to the products, failure to comply
with procedures in Agilent product user guides, or use of the
products in violation of applicable laws, rules or regulations.
Cleaning/Recycling the Product
To clean the unit, disconnect the power and wipe down with a
damp, lint-free cloth. For recycling, contact your local Agilent
sales office.
Liquid Spills
Do not spill liquids on the MS.
Moving or Storing the MS
The best way to keep your MS functioning properly is to keep it
pumped down and hot, with carrier gas flow. If you plan to
move or store your MS, a few additional precautions are
required. The MS must remain upright at all times; this requires
special caution when moving. The MS should not be left vented
to atmosphere for long periods. For more information, see “To
Move or Store the MS” in the Agilent 7200 Q-TOF GC/MS
Troubleshooting and Maintenance Manual.
Operation Manual
21
1
22
Introduction
Moving or Storing the MS
Operation Manual
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
2
Installing GC Columns
Columns 24
To Install a Capillary Column in a Split/Splitless Inlet 27
To Condition a Capillary Column 31
To Install a Capillary Column in the GC/MS Interface 33
Before you can operate your GC/MS system, you must select,
install, and condition a GC column. This chapter shows you how
to install and condition a column.
Agilent Technologies
23
2
Installing GC Columns
Columns
Columns
Many types of GC columns can be used with the MS, but there
are some restrictions.
During tuning or data acquisition the rate of column flow into
the MS should not exceed the maximum recommended flow.
Therefore, there are limits to column length and flow. Exceeding
recommended flow will result in degradation of mass spectral
and sensitivity performance.
Remember that column flows vary greatly with oven
temperature. See “To Calibrate the Column” on page 51 for
instructions on how to measure actual flow in your column. Use
the flow calculator in the Agilent Instrument Utilities software,
and Table 2 to determine an acceptable column flow. For
expected column outlet flow pressures, use the values shown in
Table 3 for EI mode and Table 6 for CI mode.
Table 2
Gas flows
Feature
High-vacuum pump 1
Split flow turbo
High-vacuum pump 2
Split flow turbo
High-vacuum pump 3
Turbo
Optimal carrier gas flow, mL/min
1.0 to 1.5
Reagent gas flow, mL/min
1 to 2
Collision cell gas flow
1.5
Maximum recommended gas flow, mL/min*
2.0
Maximum gas flow, mL/min†
2.4
Maximum column id
0.32 mm (30 m length)
* Total gas flow into the MS = column flow + collision cell gas flow + reagent gas
flow (if applicable) + Agilent Quick Swap flow (if applicable)
† Expect degradation of spectral performance and sensitivity.
24
Operation Manual
Installing GC Columns
Columns
2
Conditioning columns
Conditioning a column before it is connected to the GC/MS
interface is essential.
A small portion of the capillary column stationary phase is
often carried away by the carrier gas. This is called column
bleed. Column bleed deposits traces of the stationary phase in
the MS ion source. This decreases MS sensitivity and makes
cleaning the ion source necessary.
Column bleed is most common in new or poorly cross-linked
columns. It is much worse if there are traces of oxygen in the
carrier gas when the column is heated. To minimize column
bleed, all capillary columns should be conditioned before they
are installed in the GC/MS interface.
Conditioning ferrules
Heating ferrules to their maximum expected operating
temperature a few times before they are installed can reduce
chemical bleed from the ferrules.
Operation Manual
25
2
Installing GC Columns
Columns
Tips and hints
• The column installation procedure for the 7200 Q-TOF
GC/MS is different from that for other MSs. Using the
procedure from another instrument may not work and may
damage the column or the MS.
• You can remove old ferrules from column nuts with an
ordinary pushpin.
• Always use carrier gas that is at least 99.9995% pure.
• Because of thermal expansion, new ferrules may loosen after
heating and cooling a few times. Check for tightness after two
or three heating cycles.
• Always wear clean gloves when handling columns, especially
the end that will be inserted into the GC/MS interface.
26
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
WA R N I N G
Always wear safety glasses when handling capillary columns. Use care to avoid
puncturing your skin with the end of the column.
Operation Manual
Installing GC Columns
To Install a Capillary Column in a Split/Splitless Inlet
2
To Install a Capillary Column in a Split/Splitless Inlet


General Materials
• Gloves, clean
• Large (8650-0030)
• Small (8650-0029)
• Metric ruler
• Septum (may be old, used inlet septum)
• Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510)
Self Tightening Column Nut Materials (Recommended)
• Self Tightening column nut (5190-6194)
• Ferrules, Vespel for Self Tightening column nut
• 5181-3323 Ferrule, 0.4mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5mm VG 0.32 col 10 pk
Traditional Universal Column Nut Materials
• 5181-8830 Universal column nut, 2 pk
• Ferrules, Vespel for universal column nut
• 5181-3323 Ferrule, 0.4mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5mm VG 0.32 col 10 pk
To install columns in other types of inlets, refer to your gas
chromatograph user information.
Procedure
WA R N I N G
The GC operates at high temperatures. In order to avoid burns, do not touch any
parts of the GC until you are sure they are cool.
1
Operation Manual
Cool the oven to room temperature.
27
2
Installing GC Columns
To Install a Capillary Column in a Split/Splitless Inlet
CAUTION
Always wear clean gloves while handling any parts that go inside the GC or analyzer
chambers.
2
Wearing clean gloves, slide a septum, column nut, and
conditioned ferrule onto the free end of the column.
Figure 2 shows a traditional inlet column nut but the nut is
similarly positioned for a self tightening column nut.

The tapered end of the ferrule should point away from the
column nut for a column attachment to an inlet.
Capillary column
Column cutter
Ferrule
Inlet column nut
Septum
Figure 2
28
Preparing a capillary column for installation (standard inlet column nut shown)
3
Use the column cutter to score the column 2 cm from the
end.
4
While holding the column against the column cutter with
your thumb, break the column against the edge of the
column cutter.
5
Inspect the end for jagged edges or burrs. If the break is not
clean and even, repeat steps 3 and 4.
Operation Manual
Installing GC Columns
To Install a Capillary Column in a Split/Splitless Inlet
6
Wipe the outside of the free end of the column with a
lint-free cloth moistened with methanol.
7
Position the septum under the column nut so that the
column extends 4 to 6 mm past the end of the ferrule
(Figure 3).
8
Insert the column in the inlet.
9
Slide the nut up the column to the inlet base and
finger-tighten the nut.
2
10 Adjust the column position so the septum is even with the
bottom of the column nut.
CAUTION
Never use a wrench to tighten a self tightening nut. This may result in damage to the
nut or instrument.
11 For the Self Tightening column nut, finger-tighten until it
begins to grip the column then turn an additional 30 to 60
degrees until tight.

For the traditional column nut tighten the nut an additional
1/4 to 1/2 turn. The column should not slide with a gentle
tug.
12 Start carrier gas flow.
13 Verify flow by submerging the free end of the column in
isopropanol. Look for bubbles.
Operation Manual
29
2
Installing GC Columns
To Install a Capillary Column in a Split/Splitless Inlet
Insulation cup
Reducing nut
Capillary column
4 to 6 mm
Ferrule (inside nut)
Inlet column nut
Septum
Figure 3
30
Installing a capillary column for a split/splitless inlet
The traditional inlet column nut is shown and the recommended self tightening inlet column nut is also provided but
not shown.
Operation Manual
Installing GC Columns
To Condition a Capillary Column
2
To Condition a Capillary Column


Materials needed
• Carrier gas, (99.9995% pure or better)
• Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510)
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
WA R N I N G
The GC operates under high temperatures. To avoid burns, do not touch any GC
parts unless you are certain they are cool.
Procedure
CAUTION
Operation Manual
1
Install the column in the GC inlet. (See “To Install a
Capillary Column in a Split/Splitless Inlet” on page 27.)
2
Set a minimum velocity of 30 cm/s, or as recommended by
the column manufacturer. Allow gas to flow through the
column at room temperature for 15 to 30 minutes to remove
air.
3
Program the oven from room temperature to the maximum
temperature limit for the column.
4
Increase the temperature at a rate of 10 to 15 °C/min.
5
Hold at the maximum temperature for 30 minutes.
Never exceed the maximum column temperature, either in the GC/MS interface,
the GC oven, or the inlet.
6
Set the GC oven temperature to 30 °C and wait for the GC to
become ready.
7
Attach the column to the GC interface. (See “To Install a
Capillary Column in the GC/MS Interface” on page 33.)
31
2
Installing GC Columns
To Condition a Capillary Column
For more information about installing a capillary column, refer
to Optimizing Splitless Injections on Your GC for High
Performance MS Analysis, Agilent Technologies publication
number 5988-9944EN.
32
Operation Manual
Installing GC Columns
To Install a Capillary Column in the GC/MS Interface
2
To Install a Capillary Column in the GC/MS Interface


This procedure is for the installation of a capillary column
directly into the analyzer using the Agilent recommended
self-tightening column nut.
Materials needed
• Column cutter, ceramic (5181-8836) or diamond (5183-4620)
• Flashlight
• Magnifying loupe
• Gloves, clean
• Large (8650-0030)
• Small (8650-0029)
• Septum (may be old, used inlet septum)
• Safety glasses
• Column install tool (G3850-60014)
Self Tightening Column Nut Materials (Recommended)
• Self Tightening column nut (5190-5233)
• Ferrules, Vespel for Self Tightening column nut
• 5181-3323 Ferrule, 0.4mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5mm VG 0.32 col 10 pk
Traditional MS Interface Nut Materials
• MS Interface column nut (05988-20066)
• Ferrules, Vespel for universal column nut
• 5181-3323 Ferrule, 0.4mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5mm VG 0.32 col 10 pk
Operation Manual
33
2
Installing GC Columns
To Install a Capillary Column in the GC/MS Interface
Procedure
CAUTION
Always wear clean gloves while handling any parts that go inside the GC or the
analyzer chambers.
1
WA R N I N G
The analyzer, GC/MS interface, and other components in the analyzer chamber
operate at very high temperatures. Do not touch any part until you are sure it is
cool.
WA R N I N G
Dangerous voltages exist inside the analyzer chamber, which can result in fatal
injury. Do not open the analyzer chamber door for any reason. If access is ever
required, trained service personnel must first disconnect the instrument from the
building power source.
2
WA R N I N G
34
Condition the column. (See “To Condition a Capillary
Column” on page 31.)
Vent the MS. To vent the MS, see “To Vent the MS” on
page 62.
The GC operates under high temperatures. To avoid burns, do not touch any GC
parts unless you are certain they are cool.
3
Slide the Self Tightening or standard column interface nut
and conditioned ferrule onto the free end of the GC column.
The tapered end of the ferrule must point towards the nut.
4
Insert the column into the column install pre-swaging tool,
and allow the end of the column to project past the end of
the tool.
5
Use the column cutter to score the column 2 cm from its
end.
Operation Manual
Installing GC Columns
To Install a Capillary Column in the GC/MS Interface
2
6
While holding the column against the column cutter with
your thumb, break the column against the edge of the
column cutter.
7
Inspect the end for jagged edges or burrs. If the break is not
clean and even, repeat steps 5 and 6.
8
Wipe the outside of the free end of the column with a
lint-free cloth moistened with methanol.
9
Slide the column so that the end projects 4–5 mm past the
end of the column install pre-swaging tool.
10 For the Self Tightening column nut, finger-tighten until it
begins to grip the column then turn an additional 30 to 60
degrees until tight.

For the traditional column nut tighten the nut an additional
1/4 to 1/2 turn. The column should not slide with a gentle
tug.
11 Loosen the column nut and remove the column from the
tool.
12 Slide the column into the GC/MS interface.
13 Hand-tighten the nut. Make sure the position of the column
does not change as you tighten the nut.
14 Check the GC oven to be sure that the column does not
touch the oven walls.
15 Check the nut’s tightness after one or two heat cycles;
re-tighten as appropriate.
Operation Manual
35
2
36
Installing GC Columns
To Install a Capillary Column in the GC/MS Interface
Operation Manual
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
3
Operating in Electron Impact
(EI) Mode
Operating the MS from the Data System 38
The GC/MS Interface 39
Before You Turn On the MS 41
Pumping Down 42
Controlling Temperatures 42
Controlling Column Flow 42
Controlling Collision Cell Flow 43
Venting the MS 44
Typical Vacuum Pressures in EI Mode 45
To Set Monitors for Temperature and Vacuum Status 46
To Set the MS Analyzer Temperature 48
To Set the GC/MS Interface Temperature from the
MassHunter Workstation 50
To Calibrate the Column 51
To Configure the Collision Cell Gas 53
To Set the Collision Cell Gas Flow Rate 54
To Autotune the MS for EI Mode 55
To Remove the Upper RIS Cover 57
To Open the Analyzer Cover for Access to the Analyzer
Sideplate 58
To Pump Down the MS 59
To Vent the MS 62
Agilent Technologies
37
3
Operating in Electron Impact (EI) Mode
Operating the MS from the Data System
This chapter will explain how to perform some routine
operating procedures for the 7200 Accurate-Mass Q-TOF GC/MS
in EI mode.
Operating the MS from the Data System
The Agilent MassHunter Data Acquisition Workstation
automates tasks such as pumping down, removing the ion
source, monitoring settings, setting temperatures, tuning, and
venting the MS. These tasks are described in this chapter.
Additional information is described in the manuals and online
help supplied with the MassHunter Workstation software.
CAUTION
The software and firmware are revised periodically. If the steps in these procedures
do not match your MassHunter Workstation software, refer to the manuals and
online help supplied with the software for more information.
Your G3851BA 7200 Q-TOF GC/MS provides the capability of
operating in either EI or CI modes, using the new RIS
technology. You must specify the type of ionization you are
using in the Acquisition software tune file used by your method.
38
Operation Manual
Operating in Electron Impact (EI) Mode
The GC/MS Interface
3
The GC/MS Interface
The GC/MS interface (Figure 4) is a heated conduit into the MS
for the capillary column. The interface is bolted onto the right
side of the front analyzer chamber and has an O-ring seal. It has
a protective insulated cover that should be left in place.
One end of the GC/MS interface passes through the side of the
gas chromatograph and extends into the GC oven. This end is
threaded to allow connection of the column with a nut and
ferrule. The other end of the interface fits into the ion source.
The last 4 to 5 mm of the capillary column extends past the end
of the guide tube and into the ionization chamber. When
changing the removable ion source, the interface is
automatically retracted from the ion source by the MassHunter
software. This allows the ion source to slide freely in and out of
the analyzer chamber.
The GC/MS interface is heated by an electric cartridge heater.
Normally, the heater is powered and controlled by the Thermal
Aux #2 heated zone of the GC. The interface temperature can be
set from the MassHunter Workstation or from the gas
chromatograph keypad. A sensor (thermocouple) in the
interface monitors the temperature.
The GC/MS interface generally operates in the 250 to 350 C
range. Subject to that restriction, the interface temperature
should be slightly higher than the maximum GC oven
temperature, but never higher than the maximum column
temperature.
See also
“To Install a Capillary Column in the GC/MS Interface” on
page 33.
WA R N I N G
Operation Manual
The GC/MS interface operates at high temperatures. If you touch it when it is
hot, it will burn you.
39
3
Operating in Electron Impact (EI) Mode
The GC/MS Interface
Spring-loaded tip
seal entrance to
ion source
Column nut
MS
GC oven
IRM calibrant in
Heater sensor assembly
Column end protrudes 4 to 5mm into the ionization chamber.
Column not shown
Figure 4
40
The GC/MS interface
Operation Manual
Operating in Electron Impact (EI) Mode
Before You Turn On the MS
3
Before You Turn On the MS
Verify the following before you turn on or attempt to operate the
MS.
• All vacuum seals and fittings must be in place and fastened
correctly. The analyzer plate thumbscrew should be
unfastened, unless hazardous carrier or reagent gases are
being used.
• The MS is connected to a grounded power source.
• The GC/MS interface extends into the GC oven.
• A conditioned capillary column is installed in the GC inlet
and in the GC/MS interface.
• The GC is on, but the heated zones for the GC/MS interface,
the GC inlet, and the oven are off.
• Carrier gas of at least 99.9995% purity is plumbed to the GC
with the recommended traps.
• The use of hydrogen gas is specifically prohibited with this
product.
• The foreline pump exhaust is properly vented.
WA R N I N G
The exhaust from the foreline pump contains solvents and the chemicals you are
analyzing. The standard foreline pump, also exhausts traces of pump oil. If you
are using toxic solvents or analyzing toxic chemicals, attach a hose (11-mm id)
to the oil mist filter to take the foreline pump exhaust outside or to a fume
(exhaust) hood. Be sure to comply with local regulations. The oil mist filter
supplied with the standard pump stops only pump oil. It does not trap or filter out
toxic chemicals.
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
Operation Manual
41
3
Operating in Electron Impact (EI) Mode
Pumping Down
Pumping Down
Pumping down is only required if the analyzer was vented. It is
not required for changing the ion source. 

The data system helps you pump down the MS. The process is
mostly automated. When you turn on the main power switch
(while pressing on the analyzer sideplate), the MS pumps down
by itself. The data system software monitors and displays
system status during pumpdown. When the pressure is low
enough, the program turns on the ion source and mass filter
heaters and prompts you to turn on the GC/MS interface heater.
The MS will shut down if it cannot pump down correctly.
Using the MS monitors, the data system can display:
• Motor speed for each MS turbo pump
• Analyzer chamber pressure (vacuum)
• Quadrupole and ion source temperatures
Controlling Temperatures
MS temperatures are controlled through the data system. The
MS has independent heaters and temperature sensors for the
ion source and the quadrupole mass filter. You can adjust the
setpoints and view these temperatures from the data system
The GC/MS interface heater is powered and controlled by the
Thermal Aux #2 heated zone of the GC. The GC/MS interface
temperature can be set and monitored from the data system or
from the GC keypad.
Controlling Column Flow
Carrier gas flow is controlled by column inlet pressure in the
GC. For a given inlet pressure, column flow will decrease as the
GC oven temperature increases. With electronic pneumatic
control (EPC) and the column mode set to Constant Flow, the
same column flow is maintained regardless of temperature.
42
Operation Manual
Operating in Electron Impact (EI) Mode
Controlling Collision Cell Flow
3
The MS can be used to measure actual column flow. You inject a
small amount of air or other unretained chemical and time how
long it takes to reach the MS. With this time measurement, you
can calculate the column flow. See “To Calibrate the Column” on
page 51.
Controlling Collision Cell Flow
The collision cell gas flow rate is controlled by an EPC module
located in the GC. The collision cell gas flow consists of
nitrogen. The gas pressure at the EPC outlet controls the flow of
the gas. This pressure is controlled by the MassHunter Data
Acquisition Workstation or directly at the GC keypad. See “To
Set the Collision Cell Gas Flow Rate” on page 54.
Operation Manual
43
3
Operating in Electron Impact (EI) Mode
Venting the MS
Venting the MS
A program in the data system automates the venting process. It
turns off the GC and MS heaters and the turbo pump at the
correct time.
The Fast Vent feature loads a user-defined GC method that sets
an oven temperature, turns off the transfer line heater and sets
the column flow to a user predefined level.
The MS will be damaged by incorrect venting. A turbo pump will
be damaged if it is vented while spinning at more than 50% of its
normal operating speed.
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
CAUTION
Never vent the MS by allowing air in through either end of the foreline hose. Use
the vent valve or remove the column nut and column.
Do not exceed the maximum recommended total gas flow. See Table 2.
44
Operation Manual
Operating in Electron Impact (EI) Mode
Typical Vacuum Pressures in EI Mode
3
Typical Vacuum Pressures in EI Mode
The largest influences on operating pressure in EI mode are the
carrier gas (column) and collision cell gas flows. Table 3 lists
typical pressures for various helium and nitrogen collision cell
gas flows. These pressures are approximate and will vary from
instrument to instrument by as much as 30%.
Table 3
Influence of carrier and collision cell gas flows on vacuum
CC Gas On
N2 = 1.5 mL/min
CC Gas Off
Column Flow
(mL/min)
Rough Vac
Quad Vac
TOF Vac
Rough Vac
Quad Vac
TOF Vac
0.5
1.16 * 10-1
3.41 * 10-5
4.20* 10-7
8.29 * 10-2
3.17 * 10-7
2.15 * 10-7
0.7
1.18 * 10-1
3.41 * 10-5
4.20 * 10-7
8.67 * 10-2
3.45 * 10-7
2.15 * 10-7
1
1.22 * 10-1
3.43 * 10-5
4.22 * 10-7
9.17 * 10-2
3.79 * 10-7
2.16 * 10-7
1.2
1.24 * 10-1
3.43 * 10-5
4.22 * 10-7
9.49 * 10-2
4.06 * 10-7
2.16 * 10-7
2
1.32 * 10-1
3.44 * 10-5
4.22 * 10-7
1.07 * 10-1
5.17 * 10-7
2.17 * 10-7
3
1.42 * 10-1
3.44 * 10-5
4.25 * 10-7
1.19 * 10-1
6.51 * 10-7
2.20 * 10-7
4
1.50 * 10-1
3.46 * 10-5
4.27 * 10-7
1.29 * 10-1
7.84 * 10-7
2.21 * 10-7
If the pressure is consistently higher than those listed, refer to
the online help in the MassHunter Workstation software for
information on troubleshooting air leaks and other vacuum
problems.
Operation Manual
45
3
Operating in Electron Impact (EI) Mode
To Set Monitors for Temperature and Vacuum Status
To Set Monitors for Temperature and Vacuum Status
A monitor displays the current value of a single instrument
parameter. They can be added to the standard instrument
control window. Monitors can be set to change color if the
actual parameter varies beyond a user-determined limit from its
setpoint.
Procedure
1
Select Instrument > Edit Monitors to display the Select Monitors
dialog box. See Figure 5.
Figure 5
46
Select Monitors dialog box
Operation Manual
Operating in Electron Impact (EI) Mode
To Set Monitors for Temperature and Vacuum Status
Figure 6
3
2
In the Available Monitors column, select a monitor and click
the Add button to move the selected monitor to the Selected
Monitors column.
3
Select any other monitors you want and add them to the
Selected Monitors column.
4
Click OK. The new monitors will be stacked on top of each
other in the lower right corner of the Instrument Control
window.
5
Select Window > Arrange Monitors, or click and drag each
monitor to the desired position. See Figure 6 for one way of
arranging the monitors.
6
To make the new settings part of the method, select Save
from the Method menu.
Arranging monitors
Operation Manual
47
3
Operating in Electron Impact (EI) Mode
To Set the MS Analyzer Temperature
To Set the MS Analyzer Temperature
Setpoints for the MS ion source and quad temperatures are
stored in the current tune file. When a method is loaded, the
setpoints in the tune file associated with that method are
downloaded automatically.
Procedure
Table 4
48
1
In Instrument Control panel, select the MS Tune icon to display
the Tune dialog box. Select the Manual Tune tab then select
the Ion Source tab to display the ion source parameters.
2
Enter the temperature setpoint in the Source Temp field. See
Table 4 for recommended setpoints.
3
Select the Quadrupole tab to display the MS parameters.
4
Enter the temperature setpoint in the Quad Temp field. See
Table 4 for recommended setpoints.
5
Select the Files and Reports tab then click the Save button to
save the tune file with these changes.
Recommended temperature settings
Zone
EI operation
MS Source
230 °C
MS Quad
150 °C
Operation Manual
Operating in Electron Impact (EI) Mode
To Set the MS Analyzer Temperature
Figure 7
3
Setting temperatures
The GC/MS interface, ion source, and the MS quadrupole
heated zones interact. The analyzer heater may not be able to
accurately control temperature if the setpoint for one zone is
much different from that of an adjacent zone.
WA R N I N G
Operation Manual
The software will not allow you to exceed 200 °C for the quadrupole or 350 °C for
the ion source.
49
3
Operating in Electron Impact (EI) Mode
To Set the GC/MS Interface Temperature from the MassHunter Workstation
To Set the GC/MS Interface Temperature from the MassHunter
Workstation
You can also use the GC Control panel to perform this task.
Procedure
Figure 8
Select Instrument > GC Parameters from the Instrument Control
panel.
2
Click the Aux Heaters icon to edit the interface temperature
(Figure 8). This example has the GC/MS interface
temperature configured as Thermal Aux 2.
Setting the interface temperature
CAUTION
50
1
Make sure that the carrier gas is turned on and the column has been purged of air
before heating the GC/MS interface or the GC oven.
Operation Manual
Operating in Electron Impact (EI) Mode
To Calibrate the Column
CAUTION
3
When setting the GC/MS interface temperature, never exceed the maximum for
your column.
3
Check the heater On and enter the setpoint in the Value °C
column. The typical setpoint is 280 °C. The limits are 0 °C
to 400 °C. A setpoint below ambient temperature turns off
the interface heater.
4
Click Apply to download setpoints or click OK to download
setpoints and close the window.
5
To make the new settings part of the method, select Save
from the Method menu.
To Calibrate the Column
Capillary columns must be calibrated prior to use with the MS.
Procedure
1
Set Data Acquisition for splitless manual injection and set
up a real time plot to monitor m/z 28.
2
Press [Prep Run] on the GC keypad.
3
Inject 1 µL of air into the GC inlet and press [Start Run]
4
Wait until a peak elutes at m/z 28. Note the retention time.
5
In the Instrument Control panel, select
6
Select the Configuration tab.
7
Select the Column tab and from the table, then select the
column to be calibrated and click Calibrate.
8
Select the Calc Length button.
9
In the Calculate Column Length dialog box, enter the recorded
retention time in the Holdup Time of an Unretained Peak field.
.
10 Verify that the other parameters listed (temperature, inlet
and outlet pressures, and gas type) are those used in the
method to determine the holdup time. Change any
Operation Manual
51
3
Operating in Electron Impact (EI) Mode
To Calibrate the Column
parameters that are different than those used in your
method.
Figure 9
Calculate Column Length dialog box
11 When the new column length appears, click OK to save the
changes.
12 Click OK on the Calibrate Columns screen to save the
calibration.
52
Operation Manual
Operating in Electron Impact (EI) Mode
To Configure the Collision Cell Gas
3
To Configure the Collision Cell Gas
1
From the MassHunter Data Acquisition Workstation Instrument
Control panel, select
2
Figure 10
.
Click the Configuration icon and select the Modules tab to
display the screen. See Figure 10.
Configure collision cell gas
Operation Manual
3
From the Collision Cell EPC drop-down menu, select N2 as the
collision cell gas.
4
Click OK to save the configuration.
53
3
Operating in Electron Impact (EI) Mode
To Set the Collision Cell Gas Flow Rate
To Set the Collision Cell Gas Flow Rate
Figure 11
54
1
From the MassHunter Data Acquisition Workstation
Instrument Control panel, select Instrument > GC Parameters.
2
Click the Columns icon to display control parameter entry
screen for column and Aux flow modules. See Figure 11.
3
Select Collision Cell EPC in the Selection list.
4
Enter the required gas flow rates in the appropriate fields.
5
Click the N2 Collision Gas check box to allow the N2 collision
gas flow.
6
Click Apply to download the setpoints or OK to download the
setpoints and close the window.
7
To make the new settings part of the method, select Save
from the Method menu.
Setting collision cell gas flow rate
Operation Manual
Operating in Electron Impact (EI) Mode
To Autotune the MS for EI Mode
3
To Autotune the MS for EI Mode
The MS can be tuned using the MassHunter Workstation
software.
Procedure
1
Set the system to the same conditions (GC oven
temperature and column flow, and MS analyzer
temperature) that will be used for data acquisition.
2
In the Instrument Control panel, click the MS Tune icon to
display the GC/Q-TOF Tune dialog box.
3
The current tune file is displayed in the upper left corner of
the GC/Q-TOF Tune dialog box. Verify that the correct tune
file is loaded.
4
If necessary, load a new tune file by clicking on the Files and
Report tab then click on the Load button in the Tune File area.
Select a tune file and click the OK button.
The tune file must match the type of ion source in the
analyzer. If you are using an EI ion source, select a tune file
created for an EI ion source.
Operation Manual
5
Click the Autotune tab and select the Tune from default settings
check box if you are restarting the system after a system
vent, major servicing, or a power outage. If you clear the
Tune from default settings box, the autotune process starts
using the previous tune values.
6
Select Save tune file when done check box to save the new tune
parameters generated by the autotune. Do not select this
item if you want to review the autotune report before saving
the newly generated tune parameters.
7
Select the Print autotune report check box to automatically
print a tune report.
8
Click the Autotune button to start the autotune. The Status
line displays the current step in the autotune process and
the plot of the tuned parameter for that step is shown in the
top graph. If specified above, at the completion of the
autotune, a Tune Report is printed.
55
3
Operating in Electron Impact (EI) Mode
To Autotune the MS for EI Mode
To stop the autotune before it completes the automatic
parameter selection, click the Abort Tune button. The
parameters from the last successful autotune are used.
9
Review the Tune Report. If the results are acceptable and
you did not select the Save tune file when done check box, save
the autotune by clicking the Files and Report tab, then click
the Save button.
See the manuals or online help provided with your MassHunter
Data Acquisition Workstation software for additional
information about tuning.
Figure 12
56
EI Autotune
Operation Manual
Operating in Electron Impact (EI) Mode
To Remove the Upper RIS Cover
3
To Remove the Upper RIS Cover


The upper RIS cover is in front of the instrument (Figure 13).
Remove it to access the latches on the analyzer cover, attach the
RIS probe, or access the EI calibration vial. Do not remove the
upper RIS cover for any other reasons.
Procedure
1 Grasp the cover by the outside corners.
2 Pull the cover straight up, and remove it from the
instrument.
Figure 13
Operation Manual
Upper RIS cover
57
3
Operating in Electron Impact (EI) Mode
To Open the Analyzer Cover for Access to the Analyzer Sideplate
To Open the Analyzer Cover for Access to the Analyzer Sideplate


Open the analyzer cover (Figure 14) to access the analyzer
sideplate only. This is necessary during pump down or to access
the analyzer sideplate thumbscrews. You should not open the
analyzer cover for any other reason.
Procedure
1
Remove the upper RIS cover to expose the analyzer cover
latches. See “To Remove the Upper RIS Cover” on page 57.
2
Open the latches on the analyzer cover at the front of the
instrument.
3
Swing the analyzer cover open.
Analyzer cover
Upper RIS cover
Figure 14
58
Covers
Operation Manual
Operating in Electron Impact (EI) Mode
To Pump Down the MS
3
To Pump Down the MS
WA R N I N G
Make sure your MS meets all the conditions listed in the introduction to this
chapter before starting up and pumping down the MS. Failure to do so can result
in personal injury.
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
WA R N I N G
Dangerous voltages exist inside the analyzer chamber, which can result in fatal
injury. Do not open the analyzer chamber door for any reason. If access is ever
required, trained service personnel must first disconnect the instrument from the
building power source.
Procedure
CAUTION
1
Open the analyzer cover to access the analyzer quad driver
board. See “To Open the Analyzer Cover for Access to the
Analyzer Sideplate” on page 58.
2
Plug the power cord into a grounded electrical outlet.
3
Turn on the Q-TOF power switch (Figure 14).
4
Press lightly on the metal box on the quad driver board to
ensure a correct seal.
Do not push on the filament board safety cover while pressing on the analyzer
board. This cover was not designed to withstand this type of pressure.
The foreline pump will make a gurgling noise. This noise
should stop within a minute. If the noise continues, there is
a large air leak in your system, probably at the sideplate
seal or the interface column nut.
Operation Manual
5
Start the MassHunter Data Acquisition program. If the
Q-TOF was configured for both an EI and a CI ion source,
you are prompted for the ion source type that is currently
installed. Click on an EI or CI ion source type if prompted.
6
Select the MS Tune icon from the Instrument Control panel.
59
3
Operating in Electron Impact (EI) Mode
To Pump Down the MS
Figure 15
7
Select the Vacuum Control tab.
8
Click the Pumpdown button.
Vacuum Control tab
CAUTION
Do not turn on any GC heated zones until carrier gas flow is on. Heating a column
with no carrier gas flow will damage the column.
Within 10 to 15 minutes the turbo pump speed should be up to
80% (Figure 15). The pump speed should eventually reach 95%.
If these conditions are not met, the MS electronics will shut off
the foreline pump. In order to recover from this condition, you
must power cycle the MS. If the MS does not pump down
correctly, see the manual or online help for information on
troubleshooting air leaks and other vacuum problems.
9
Turn on the carrier gas flow after the vacuum pumps have
been running for 15 minutes.
10 When prompted, turn on the GC/MS interface heater and
GC oven. Click OK when you have done so. The software will
turn on the ion source and mass filter (quad) heater. The
temperature setpoints are stored in the current autotune
file.
60
Operation Manual
Operating in Electron Impact (EI) Mode
To Pump Down the MS
3
11 After the message Okay to run appears, wait 2 hours for the
MS to reach thermal equilibrium. Data acquired before the
MS has reached thermal equilibrium may not be
reproducible.
12 Tune the MS. (See “To Autotune the MS for EI Mode” on
page 55 or “To Perform a CI Autotune” on page 79.)
Operation Manual
61
3
Operating in Electron Impact (EI) Mode
To Vent the MS
To Vent the MS
Procedure
62
1
Click the MS Tune icon from the Instrument Control panel.
2
Select the Vacuum Control tab. See Figure 15.
3
Set the GC/MS interface heater and the GC oven
temperatures to ambient (room temperature).
4
When the GC temperatures have reached 30 °C, turn off the
flow of carrier gas.
5
Click the Vent button.
WA R N I N G
The use of hydrogen gas is specifically prohibited with this product.
CAUTION
Be sure the GC oven and the GC/MS interface are cool before turning off carrier
gas flow.
6
Turn off the MS by pressing the power switch. (See
Figure 1.)
7
Unplug the MS power cord.
WA R N I N G
Allow the analyzer to cool to near room temperature before touching it.
CAUTION
When the MS is vented, do not put the Workstation into Instrument Control view.
Doing so will turn on the interface heater, which can damage the column.
Operation Manual
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
4
Operating in Chemical
Ionization (CI) Mode
Setting Up Your MS to Operate in CI Mode 64
The GC/MS Interface 65
Operating the CI MS 67
High Vacuum Pressure in CI Mode 68
Other Reagent Gases 70
CI Autotune 72
The Flow Control Module 73
To Switch from the EI Mode to CI Mode 74
To Operate the Reagent Gas Flow Control Module 76
To Set a Reagent Gas Flow 78
To Perform a CI Autotune 79
This chapter provides information and instructions for
operating the 7200 Q-TOF GC/MS system in Chemical Ionization
(CI) mode. Most of the information in the preceding chapter is
also relevant.
Most of the material is related to methane chemical ionization
but one section discusses the use of other reagent gases.
The software contains instructions for setting the reagent gas
flow and for performing CI autotunes. Autotunes are provided
for positive CI (PCI) with methane reagent gas and for negative
CI (NCI) with any reagent gas.
Agilent Technologies
63
4
Operating in Chemical Ionization (CI) Mode
Setting Up Your MS to Operate in CI Mode
Setting Up Your MS to Operate in CI Mode
Setting up your MS for operation in CI mode requires special
care to avoid contamination and air leaks.
• Always use the highest purity methane (and other reagent
gases, if applicable). Methane must be at least 99.9995% pure.
• Always verify the MS is performing well in EI mode before
switching to CI.
• Make sure the CI ion source is installed.
• Make sure the reagent gas plumbing has no air leaks. This is
determined in PCI mode, checking for m/z 32 after the
methane pretune.
• Make sure the reagent gas inlet line is equipped with gas
purifiers (not applicable for ammonia).
64
Operation Manual
Operating in Chemical Ionization (CI) Mode
The GC/MS Interface
4
The GC/MS Interface
The GC/MS interface (Figure 16) is a heated conduit into the MS
for the capillary column. It is bolted onto the right side of the
analyzer chamber, with an O-ring seal and has a protective
insulated cover which should be left in place.
One end of the interface passes through the side of the GC and
extends into the oven. It is threaded to allow connection of the
column with a nut and ferrule. The other end of the interface
fits into the ion source. The last 4 to 5 millimeters of the
capillary column extend past the end of the guide tube and into
the ionization chamber. When changing the removable ion
source, the interface is automatically retracted from the ion
source with the MassHunter software. This allows the source to
slide freely in and out of the analyzer chamber.
For CI operating mode, reagent gas is also plumbed into the
interface. A tip seal keeps reagent gases from leaking out
around the tip. The reagent gas enters the interface body and
mixes with carrier gas and sample in the ion source.
The GC/MS interface is heated by an electric cartridge heater.
Normally, the heater is powered and controlled by the Thermal
Aux #2 heated zone of the GC. The interface temperature can be
set from the MassHunter Workstation or from the gas
chromatograph keypad. A sensor (thermocouple) in the
interface monitors the temperature.
This interface is also be used for EI operation.
The interface should be operated in the 250  to 350 C range.
Subject to that restriction, the interface temperature should be
slightly higher than the maximum GC oven temperature, but
never higher than the maximum column temperature.
See Also
“To Install a Capillary Column in the GC/MS Interface” on
page 33.
Operation Manual
65
4
Operating in Chemical Ionization (CI) Mode
The GC/MS Interface
CAUTION
Never exceed the maximum column temperature, either in the GC/MS interface,
the GC oven, or the inlet.
WA R N I N G
The GC/MS interface operates at high temperatures. If you touch it when it is
hot, it will burn you.
Column nut
Spring-loaded tip
seal entrance to
ion source
MS
GC oven
Reagent gas and
IRM calibrant in
Heater sensor assembly
Column not shown
Figure 16
66
The GC/MS interface
Operation Manual
Operating in Chemical Ionization (CI) Mode
Operating the CI MS
4
Operating the CI MS
Operating your GC/MS in the CI mode is slightly more
complicated than operating in the EI mode. After tuning, gas
flow, temperatures (Table 5), and electron energy may need to
be optimized for your specific analyte.
Table 5
Temperatures for CI operation
Ion source
Analyzer
GC/MS interface
PCI
300 °C
150 °C
280 °C
NCI
150 °C
150 °C
280 °C
Start the system in CI mode
When starting up the system you may begin in either PCI or NCI
mode. Depending upon the application, use the following
reagent gas flowrates during system startup:
• PCI mode set reagent gas flow to 20 (1 mL/min)
• NCI mode set reagent gas flow to 40 (2 mL/min)
Operation Manual
67
4
Operating in Chemical Ionization (CI) Mode
High Vacuum Pressure in CI Mode
High Vacuum Pressure in CI Mode
The largest influences on operating pressure in CI mode are the
reagent and collision cell gas flows. Table 6 lists typical
pressures for various reagent gas flows, depending upon the
collision cell gas flowrate. Familiarize yourself with the
measurements on your system under operating conditions and
watch for changes that may indicate a vacuum or gas flow
problem. Measurements will vary by as much as 30% from one
MS to the next.
68
Operation Manual
Operating in Chemical Ionization (CI) Mode
High Vacuum Pressure in CI Mode
4
Analyzer vacuum with reagent gas flowing
Note that the mass flow controller (MFC) is calibrated for
methane and the vacuum gauge is calibrated for nitrogen, so
these measurements are not accurate, but are intended as a
guide to typical observed readings (Table 6). They were taken
with the following set of conditions. Note that these are typical
PCI temperatures:
Source temperature
Quad temperature
Interface temperature
Inlet
Oven
Helium carrier gas flow
Table 6
230 °C
150 °C
280 °C
250 °C
100 °C
1 mL/min
Typical analyzer vacuum with reagent gas flow
Collision cell gas flow off
N2 = 0 mL/min
Collision cell gas flow on
N2 = 1.5 mL/min
MFC (%) Rough Pump
(mTorr)
Quadrupole
(Torr)
Flight Tube
(Torr)
Rough Pump
(mTorr)
Quadrupole
(Torr)
Flight Tube
(Torr)
0
1.36e+02
3.62e-05
3.35e-07
9.13e+01
5.98e-07
1.64e-07
10
1.36+02
3.62e-05
3.37e-07
1.14e+01
1.27e-06
1.65e-07
15
1.43+02
3.66e-05
3.37e-07
1.23e+01
1.62e-06
1.67e-07
20
1.5+02
3.71e-05
3.39e-07
1.31e+01
1.96e-06
1.67e-07
25
1.57+02
3.73e-05
3.41e-07
1.39e+01
2.32e-06
1.70e-07
30
1.63+02
3.77e-05
3.41e-07
1.46e+01
2.64e-06
1.71e-07
35
1.69+02
3.81e-05
3.41e-07
1.52e+01
3.00e-06
1.71e-07
40
1.74+02
3.83e-05
3.43e-07
1.58e+01
3.34e-06
1.72e-07
Operation Manual
69
4
Operating in Chemical Ionization (CI) Mode
Other Reagent Gases
Other Reagent Gases
This section describes the use of isobutane or ammonia as the
reagent gas. You should be familiar with operating the
CI-equipped 7200 Q-TOF GC/MS with methane reagent gas
before attempting to use other reagent gases.
CAUTION
Do not use nitrous oxide as a reagent gas. It radically shortens the life span of the
filament.
Changing the reagent gas from methane to either isobutane or
ammonia changes the chemistry of the ionization process and
yields different ions. The principal chemical ionization
reactions encountered are described in general in the Agilent
7200 Accurate-Mass Q-TOF GC/MS Concept Guide. If you are
not experienced with chemical ionization, we suggest reviewing
that material before you proceed.
Isobutane CI
Isobutane (C4H10) is commonly used for chemical ionization
when less fragmentation is desired in the chemical ionization
spectrum. This is because the proton affinity of isobutane is
higher than that of methane; hence less energy is transferred in
the ionization reaction.
Addition and proton transfer are the ionization mechanisms
most often associated with isobutane. The sample itself
influences which mechanism dominates.
Ammonia CI
Ammonia (NH3) is commonly used for chemical ionization when
less fragmentation is desired in the chemical ionization
spectrum. This is because the proton affinity of ammonia is
higher than that of methane; hence less energy is transferred in
the ionization reaction.
70
Operation Manual
Operating in Chemical Ionization (CI) Mode
Other Reagent Gases
4
Because many compounds of interest have insufficient proton
affinities, ammonia chemical-ionization spectra often result
from the addition of NH4+ and then, in some cases, from the
subsequent loss of water. Ammonia reagent ion spectra have
principal ions at m/z 18, 35, and 52, corresponding to NH4+,
NH4(NH3)+, and NH4(NH3)2+.
CAUTION
Use of ammonia affects the maintenance requirements of the MS. See Chapter 6,
“General Maintenance”” for more information.
CAUTION
The pressure of the ammonia supply must be less than 5 psig. Higher pressures can
result in ammonia condensing from a gas to a liquid.
Always keep the ammonia tank in an upright position, below the level of the flow
module. Coil the ammonia supply tubing into several vertical loops by wrapping the
tubing around a can or bottle. This will help keep any liquid ammonia out of the flow
module.
Ammonia tends to break down vacuum pump fluids and seals.
Ammonia CI makes more frequent vacuum system maintenance
necessary. (See the Agilent 7200 Q-TOF GC/MS Troubleshooting
and Maintenance Manual.)
CAUTION
When running ammonia for 5 or more hours a day, the foreline pump must be
ballasted (flushed with air) for at least 1 hour a day to minimize damage to pump
seals. Always purge the MS with methane after flowing ammonia.
Frequently, a mixture of 5% ammonia and 95% helium or 5%
ammonia and 95% methane is used as a CI reagent gas. This is
enough ammonia to achieve good chemical ionization while
minimizing its negative effects.
Carbon dioxide CI
Carbon dioxide is often used as a reagent gas for CI. It has
obvious advantages of availability and safety.
Operation Manual
71
4
Operating in Chemical Ionization (CI) Mode
CI Autotune
CI Autotune
After the reagent gas flow is set, the lenses and electronics of
the MS should be tuned which is a good starting point for
developing your application settings. Typical CI application
settings are shown inTable 7.
Perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD) is used as
the calibrant. Instead of flooding the entire vacuum chamber,
the PFDTD is introduced directly into the ionization chamber
through the GC/MS interface by means of the gas flow control
module. There are no tune performance criteria. If CI autotune
completes, it passes.
CAUTION
Table 7
Always verify MS performance in EI before switching to CI operation.
Typical CI application settings
Parameter
Methane
Isobutane
Ammonia
EI
Ion polarity
Positive
Negative
Positive
Negative
Positive
Negative
N/A
Emission
150 A
50 A
150 A
50 A
150 A
50 A
35 A
Electron
energy
150 eV
150 eV
150 eV
150 eV
150 eV
150 eV
70 eV
Filament
1
1
1
1
1
1
1 or 2
Repeller
3V
3V
3V
3V
3V
3V
30 V
Ion focus
130 V
130 V
130 V
130 V
130 V
130 V
90 V
Entrance
lens offset
20 V
20 V
20 V
20 V
20 V
20 V
25 V
Shutoff valve
Open
Open
Open
Open
Open
Open
Closed
Suggested
flow
20%
40%
20%
40%
20%
40%
N/A
Source temp
250 °C
150 °C
250 °C
150 °C
250 °C
150 °C
230 °C
Quad temp
150 °C
150 °C
150 °C
150 °C
150 °C
150 °C
150 °C
72
Operation Manual
Operating in Chemical Ionization (CI) Mode
The Flow Control Module
Table 7
4
Typical CI application settings (continued)
Parameter
Methane
Isobutane
Ammonia
EI
Interface
temp
280 °C
280 °C
280 °C
280 °C
280 °C
280 °C
280 °C
Autotune
Yes
Yes
No
Yes
No
Yes
Yes
N/A Not available
The Flow Control Module
The CI reagent gas flow control module regulates the flow of
reagent gas into the CI GC/MS interface. The flow module
consists of a mass flow controller (MFC), gas select valves, CI
calibration valve, shutoff valve, control electronics, and
plumbing.
The instrument provides Swagelok inlet fittings for connecting
the CI reagent gas. The software refers to it as CI reagent gas.
Supply reagent gases at 20 to 25 psi (138 to 172 kPa) for
Methane.
Operation Manual
73
4
Operating in Chemical Ionization (CI) Mode
To Switch from the EI Mode to CI Mode
To Switch from the EI Mode to CI Mode
CAUTION
Always verify GC/MS performance in EI before switching to CI operation.
CAUTION
Always wear clean gloves while touching the analyzer or any other parts that go
inside the analyzer chamber.
Procedure
1
Change the source. See “To Change the Ion Source” on
page 84.
2
Load a suitable PCI or NCI method for use with the CI
source.
3
Click the MS Tune icon in the Instrument Control panel to
display the Tune dialog box and select the Autotune tab.
The method selects PCI or NCI autotune and the correct
reagent gas.
4
Select the Tune from default settings check box because you
have changed the ion source.
5
Select Print autotune report check box to automatically print a
tune report.
6
Click the Autotune button to start the autotune. At the
completion of the autotune, a Tune Report is printed.
7
Review the Tune Report. If the results are acceptable, save
the autotune by clicking the Files and Report tab, then click
the Save button.
Table 8
Reagent gas
Ion polarity
74
Default Tune Control Limits, used by CI autotune only 
Methane
Positive
Negative
Ammonia
Positive
Negative
Operation Manual
Operating in Chemical Ionization (CI) Mode
To Switch from the EI Mode to CI Mode
Table 8
4
Default Tune Control Limits, used by CI autotune only
(continued)
Reagent gas
Methane
Ammonia
Abundance target
1x106
1x106
N/A
1x106
Peakwidth target
0.7
0.7
N/A
0.7
Maximum repeller
4
4
N/A
4
Maximum emission
current, µA
240
50
N/A
50
Max electron energy, eV
240
240
N/A
240
Notes for Table 8:
• N/A Not available.
• Abundance target Adjust higher or lower to get desired
signal abundance. Higher signal abundance also gives higher
noise abundance.
• Peakwidth target Higher peakwidth values give better
sensitivity, lower values give better resolution.
• Maximum emission current Optimum emission current
maximum for NCI is very compound-specific and must be
selected empirically. Optimum emission current for
pesticides, for example, may be about 200 µA.
Operation Manual
75
4
Operating in Chemical Ionization (CI) Mode
To Operate the Reagent Gas Flow Control Module
To Operate the Reagent Gas Flow Control Module
Procedure
1
Figure 17
76
In Instrument Control panel, select the MS Tune icon to display
the GC/Q-TOF Tune dialog box. Select the Manual Tune tab then
select the Ion Source tab to display the ion source
parameters.
CI flow control
Operation Manual
Operating in Chemical Ionization (CI) Mode
To Operate the Reagent Gas Flow Control Module
2
4
Use the parameters in the CI Reagent Gas Control area to
control reagent gas flow.
CI Reagent - Selects the reagent gas from the dropdown
menu.
CI Gas Flow - Enter percent of maximum volumetric flow for
the selected reagent gas. The actual% transmitted by the
flow controller is shown next to this entry. 20% is a good
value for PCI and 40% is a good value for NCI.
Set button - Opens the selected reagent gas supply valve and
controls the reagent gas flow to the entered setpoint.
Off button - Turns off the reagent gas flow.
Purge button - Opens the selected reagent gas valve for 6
minutes to clear the system of unwanted compounds.
Pumpout button - Closes the reagent gas valve for 4 minutes
and evacuates the system of reagent gases. At the end of the
pumpout time the selected reagent gas valve opens.
Operation Manual
77
4
Operating in Chemical Ionization (CI) Mode
To Set a Reagent Gas Flow
To Set a Reagent Gas Flow
CAUTION
After the system has been switched from EI to CI mode, or vented for any other
reason, the MS must be baked out for at least 2 hours before tuning.
CAUTION
Continuing with CI autotune if the MS has an air leak or large amounts of water will
result in severe ion source contamination. If this happens, you will need to vent the
MS and clean the ion source.
Procedure
1
In Instrument Control panel, select the MS Tune icon to display
the GC/Q-TOF Tune dialog box. Select the Manual Tune tab then
select the Ion Source tab to display the ion source
parameters.
2
In the CI Reagent Gas Control area, select the CI reagent gas you
are using.
3
Enter the reagent gas flow setpoint in the CI Gas Flow field.
This value is entered as a percentage of maximum flow rate.
The recommended flow is 20% for a PCI source and 40% for
an NCI source.
4
Click the Set button. The Flow Set indication is displayed.
The reagent gas is flowing into the ion source at the rate
displayed next to the setpoint.
5
78
Click the Files and Reports tab, then click the Save button to
save your changes to the currently loaded tune file.
Operation Manual
Operating in Chemical Ionization (CI) Mode
To Perform a CI Autotune
4
To Perform a CI Autotune
CAUTION
Always verify MS performance in EI before switching to CI operation.
CAUTION
Avoid tuning more often than is absolutely necessary; this will minimize PFDTD
background noise and help prevent ion source contamination.
Procedure
Operation Manual
1
Verify that the MS performs correctly in EI mode first.
2
Click the MS Tune icon in the Instrument Control panel to
display the GC/Q-TOF Tune dialog box.
3
If necessary, load a new tune file by clicking on the Files and
Report tab then click the Load button in the Tune File area.
Select a tune file and click the OK button.

The tune file must match the type of ion source in the
analyzer. For a CI ion source select a tune file created for a
positive or negative CI source.
4
Click the Autotune tab and select PCI source for a positive CI
source or NCI source for a negative CI source.
5
Select the reagent gas you are using from the dropdown
menu in the CI Reagent Gas area.
6
If a log file and associated data files of the tune are
required, click the Files and Reports tab and in the Log Files
section, click on the Browse button to create a directory and
files for the logs. Click on the required log and data files
check boxes.
7
Click on the Manual Tune tab and select the Ion source tab. In
the CI Reagent Gas section, select the reagent gas and then
enter a CI Gas Flow rate of 20% for a PCI source or 40% for an
NCI source. Click on the Autotune tab to return to Autotune.
79
4
Operating in Chemical Ionization (CI) Mode
To Perform a CI Autotune
8
Select the Tune from default settings check box if you are
restarting the system after a system vent, major servicing,
or a power outage. If you clear the Tune from default settings
box, the Autotune process starts using previous tune values.
9
Select Save tune file when done check box to save the new tune
parameters generated by the autotune. Do not select this
item if you want to review the autotune report before saving
the newly generated tune parameters.
10 Select the Print autotune report check box to automatically
print a tune report.
11 Click the Autotune button to start the autotune. The Status
line displays the current step in the autotune process and
the plot of the tuned parameter for that step is shown in the
top graph. If specified above, at the completion of the
autotune a Tune Report is printed.
To stop the autotune before it completes the autotune
parameter selection, click the Abort Autotune button. The
parameters from the last successful autotune are used.
12 Review the Tune Report. If the results are acceptable and
you did not select the Save tune file when done check box, save
the autotune by clicking the Files and Report tab, then click
the Save button.
80
Operation Manual
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
5
Using the Removable Ion
Source
The Removable Ion Source 82
To Change the Ion Source 84
To Install the RIS Probe Extraction Tool 87
To Remove the Source from the Analyzer Chamber 89
To Change the Ion Source on the RIS Probe Extraction
Tool 91
To Install the Ion Source in the Analyzer Chamber 93
To Remove the RIS Probe Extraction Tool from the
Instrument 94
This chapter will explain how to use the features of the
removable ion source.
Agilent Technologies
81
5
Using the Removable Ion Source
The Removable Ion Source
The Removable Ion Source
The removable ion source (RIS) is a feature of the Agilent 7200
Q-TOF GC/MS that allows changing of the ion source without
venting the instrument through the use of the RIS probe
extractor tool. The source must be removed from the MS
periodically for routine cleaning and maintenance, or for
changing ionization modes, and the new RIS minimizes the
downtime necessary to complete these tasks. This process is
guided by the MassHunter Workstation software, which
performs the purging, valve operation, and pump down steps
automatically.
The RIS probe extraction tool consists of a RIS bayonet that
attaches to the source, a handle for moving the source in and
out of the instrument, and a cooling chamber for cooling the
source prior to removal (Figure 18). The entire process is
guided by the MassHunter Workstation Software.
The RIS cooling chamber is attached to the instrument to
provide a place to vent and purge the source with nitrogen
during source changing. An automatic gate valve closes off the
cooling chamber from the instrument to eliminate the need for
venting the instrument during this process. Only the small RIS
cooling chamber is vented.
CAUTION
82
The software and firmware are revised periodically. If the steps in these procedures
do not match your MassHunter Workstation software, refer to the manuals and
online help supplied with the software for more information.
Operation Manual
Using the Removable Ion Source
The Removable Ion Source
5
RIS handle
RIS cooling chamber
RIS bayonet
Figure 18
RIS probe extraction tool
Operation Manual
83
5
Using the Removable Ion Source
To Change the Ion Source
To Change the Ion Source
The steps necessary for changing the ion source are provided
here and also interactively in the MassHunter Workstation
software. The process is mostly automated, with the exception
of the use of the RIS probe extraction tool to remove and install
the ion source. Purging the chamber, cooling the source, and
pumping down are all performed with the use of the
Workstation software.


84
Procedure
1
From MassHunter Data Acquisition software control view,
click the MS Tune icon to display the GC/Q-TOF Tune dialog
box.
2
Click the Removable Ion Source tab in the GC/Q-TOF Tune
screen. (Figure 19)
Operation Manual
Using the Removable Ion Source
To Change the Ion Source
Figure 19
5
GC/Q-TOF Tune dialog box
3
Click the Begin button to purge the instrument.
4
When prompted, remove the RIS chamber door and attach
the RIS probe extraction tool. See “To Install the RIS Probe
Extraction Tool” on page 87.
5
Click Next to purge the chamber and pump down.
6
When the system is ready for source removal, click Next to
retract the transfer line and open the gate valve.
The RIS status area will note when the Gate Valve is Open and
the Transfer Line is Full Out.
7
Operation Manual
When prompted, remove the source. See “To Remove the
Source from the Analyzer Chamber” on page 89.
85
5
Using the Removable Ion Source
To Change the Ion Source
8
Once the source is retracted fully into the chamber, click
Next to close the gate valve and purge the cooling chamber.
The purge takes approximately 10 minutes.
9
When prompted, open the cooling chamber and change the
ion source. See “To Change the Ion Source on the RIS Probe
Extraction Tool” on page 91.
10 After replacing the source and securing the cooling
chamber door, click Next to purge and pump down.
11 When prompted that the system is ready for source
installation, click Next to retract the transfer line and open
the gate valve.
12 When prompted, install the ion source in the analyzer
chamber. See “To Install the Ion Source in the Analyzer
Chamber” on page 93.
13 Verify in the RIS Status that the ion source temperature
readback shows a source temperature. This ensures that the
source is fully inserted into its socket.
CAUTION
If the ion source is not fully installed, it may interfere with the gate valve as it
closes. Damage to the RIS, the valve, or the transfer line may occur.
14 Click Next to close the gate valve and vent the RIS cooling
chamber.
15 Remove the RIS probe extraction tool and replace the RIS
chamber cover. See “To Remove the RIS Probe Extraction
Tool from the Instrument” on page 94.
16 Click Next to pump down the chamber behind the RIS
chamber cover.
17 When prompted, click Finish.
86
Operation Manual
Using the Removable Ion Source
To Install the RIS Probe Extraction Tool
5
To Install the RIS Probe Extraction Tool


This procedure is part of an automated series of steps
controlled by MassHunter. Do not attempt this procedure unless
prompted by MassHunter to remove the RIS cover door.
Procedure
CAUTION
Operation Manual
1
When prompted by MassHunter, remove the upper RIS
cover (see “To Remove the Upper RIS Cover” on page 57).
2
Open the latch on the right side of the RIS cover door.
3
Swing the door open.
4
Lift the RIS cover door straight up to free it from the hinges,
and remove.
Do not leave the instrument with the RIS cover off. If you remove the cover, you
must install the RIS probe as soon as possible to minimize contamination in the
instrument.
5
Holding the RIS probe extraction tool by the handle,
position the RIS cooling chamber up against the instrument
RIS chamber. Hold the handle perpendicular to the front of
the instrument so that the outside edge of the cooling
chamber is flush with the RIS chamber opening on the front
instrument.
6
Line up the pins on the probe hinge with the slots on the
instrument hinge.
7
Lower the pins into the hinge.
8
Close the cooling chamber door, and secure the door with
the latch on the right side.
9
Return to step 5 in the “To Change the Ion Source” on
page 84.
87
5
88
Using the Removable Ion Source
To Install the RIS Probe Extraction Tool
Figure 20
RIS cover door
Figure 21
RIS probe installed
Operation Manual
Using the Removable Ion Source
To Remove the Source from the Analyzer Chamber
5
To Remove the Source from the Analyzer Chamber
This procedure is part of an automated series of steps
controlled by MassHunter. Do not attempt this procedure unless
prompted by MassHunter. The RIS Status area on the GC/Q-TOF
Tune tab must show the Gate Valve is Open and the Transfer Line is
Full Out.
Procedure


1
Holding the RIS handle, turn the alignment guide, which is
the white line on the RIS handle, to the two o’clock position
from the top of the handle. This ensures that the RIS
bayonet is aligned properly to attach to the source.
RIS
Alignment
guide 
(white line on
RIS handle)
Figure 22
RIS Alignment guide
CAUTION
While the RIS handle is fully extended, do not bump or push it from the side. Doing so
will break the seal and allow air into the cooling chamber.
CAUTION
Do not try to guide the ion source in manually. Push the RIS handle gently and allow
the RIS bayonet to slide on its own. The RIS bayonet will slide in straight if it is allowed
to move naturally.
Operation Manual
89
5
90
Using the Removable Ion Source
To Remove the Source from the Analyzer Chamber
2
Keeping the RIS handle in position, push the RIS handle
gently and allow the RIS bayonet to extend into the analyzer
chamber. Make sure the RIS handle extends fully, to ensure
that the RIS bayonet seats in the holes on the ion source
body properly.
3
When the ion source is properly seated, turn the RIS handle
counter clockwise until the alignment guide is in the twelve
o’clock position, to lock the ion source in place.
4
Pull the RIS handle toward you, keeping the alignment
guide at the twelve o’clock position, to retract the ion source
into the RIS cooling chamber.
5
Return to step 8 in the “To Change the Ion Source” on
page 84.
Operation Manual
Using the Removable Ion Source
To Change the Ion Source on the RIS Probe Extraction Tool
5
To Change the Ion Source on the RIS Probe Extraction Tool
This procedure is part of an automated series of steps
controlled by MassHunter. Do not attempt this procedure unless
prompted by MassHunter. The RIS Status area on the GC/Q-TOF
Tune tab must show the Gate Valve is Open and the RIS vacuum as
0.000 Torr.
CAUTION
If not done correctly, source maintenance can introduce contaminants into the MS.
Always wear clean rubber gloves when handling the source.


WA R N I N G
Operation Manual
1
Undo the latch on the right edge of the RIS cooling chamber.
2
Swing open the RIS cooling chamber until the RIS handle is
parallel with the front of the instrument.
3
Lock the RIS cooling chamber in the open position by
opening it enough to engage the locking pin on the hinge.
The 7200 Q-TOF GC/MS operates at high temperatures. Make sure the source is
cooled to a safe temperature before attempting to remove it from the RIS cooling
chamber.
4
Grasp the RIS handle with one hand, and the ion source
body with the other hand.
5
While holding the ion source steady, turn the RIS handle
counter clockwise so that the alignment guide is in the two
o’clock position. This guides the pin on the RIS bayonet out
of the track on the ion source body.
6
Gently pull the ion source free from the RIS bayonet and set
aside.
7
Remove the new ion source from its storage container. The
ion source remains connected to the lid. Twist the lid
clockwise to separate the ion source from the lid.
8
Turn the RIS handle so that the alignment guide is in the
two o’clock position.
91
5
Using the Removable Ion Source
To Change the Ion Source on the RIS Probe Extraction Tool
9
Guide the pin on the RIS bayonet into the tracks on the end
of the ion source body.
10 While holding the ion source securely, turn the RIS handle
counter clockwise so that the alignment guide is in the
twelve o’clock position, to lock the ion source securely on
the bayonet.
11 Retract the RIS handle fully so that the ion source is located
completely in the cooling chamber.
12 Raise the locking pin on the RIS cooling chamber hinge and
swing it shut.
13 Secure the RIS cooling chamber to the instrument with the
latch on the right side of the door.
14 Return to step 10 in the “To Change the Ion Source” on
page 84.
92
Operation Manual
Using the Removable Ion Source
To Install the Ion Source in the Analyzer Chamber
5
To Install the Ion Source in the Analyzer Chamber
This procedure is part of an automated series of steps
controlled by MassHunter. Do not attempt this procedure unless
prompted by MassHunter. The RIS Status area on the GC/Q-TOF
Tune tab must show the Gate Valve is Open and the Transfer Line is
Full Out.
CAUTION
Take care when walking past the front of the instrument when the RIS handle is
fully extended, to avoid damage to the instrument. When closed, the RIS handle
extends 48 cm (19 inches) out from the front of the instrument.
CAUTION
Do not try to guide the ion source in manually. Push the RIS handle gently and allow
the RIS bayonet to slide on its own. The RIS bayonet will slide in straight if it is
allowed to move naturally.
Procedure


Operation Manual
1
Make sure the alignment guide on the RIS handle is in the
twelve o’clock position. Push the RIS handle gently towards
the analyzer chamber and allow it to extend into the
analyzer chamber. This will seat the ion source securely into
its socket.
2
Once the RIS handle is fully extended, turn the RIS handle
clockwise until the alignment guide is in the two o’clock
position to release the ion source body from the RIS
bayonet.
3
Pull the RIS handle toward you until it is fully retracted into
the RIS cooling chamber.
4
Return to step 13 in the “To Change the Ion Source” on
page 84.
93
5
Using the Removable Ion Source
To Remove the RIS Probe Extraction Tool from the Instrument
To Remove the RIS Probe Extraction Tool from the Instrument
This procedure is part of an automated series of steps
controlled by MassHunter. Do not attempt this procedure unless
prompted by MassHunter. The RIS Status area on the GC/Q-TOF
Tune tab must show the Gate Valve is Open and the RIS vacuum as
0.000 Torr.
WA R N I N G
The 7200 Q-TOF GC/MS operates at high temperatures. Make sure the RIS
cooling chamber is at a safe temperature before attempting to remove it from the
instrument.


94
1
Undo the latch on the right side of the RIS probe extraction
tool and open the door.
2
Lift the RIS probe extraction tool up to release it from its
hinges.
3
Replace the RIS probe extraction tool with the RIS chamber
door.
4
Line up the hinge pins on the RIS chamber door with the
slots on the instrument hinge, and lower the pins into the
hinge.
5
Swing the RIS chamber door closed and secure the door
with the latch on the right side.
6
Return to step 16 in the “To Change the Ion Source” on
page 84.
Operation Manual
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
6
General Maintenance
Before Starting 96
Maintaining the Vacuum System 100
Maintaining the Analyzer 101
To Disassemble the EI Ion Source 103
To Assemble the EI Ion Source 105
To Disassemble the CI Ion Source 108
To Assemble the CI Ion Source 110
To Clean the Ion Source 112
To Remove a Filament 116
To Install a Filament 118
Agilent Technologies
95
6
General Maintenance
Before Starting
Before Starting
You can perform much of the maintenance required by your MS.
For your safety, read all of the information in this introduction
before performing any maintenance tasks.
Scheduled maintenance
Common maintenance tasks are listed in Table 9. Performing
these tasks when scheduled can reduce operating problems,
prolong system life, and reduce overall operating costs.
Keep a record of system performance (tune reports) and
maintenance operations performed. This makes it easier to
identify variations from normal operation and to take
corrective action.
Table 9
Maintenance schedule
Task
Every week
Every 6 months
Every year
Tune the MS
Check the foreline pump oil level
As needed
X
X
Check the calibration vial(s)
X
Replace the foreline pump oil*
X
Clean the ion source
X
Check the carrier gas trap(s) on the GC and MS
X
Replace the worn out parts
X
Replace gasket on RIS probe
Check the IRM vial
Replace GC gas supplies
X
X
X
X
* Or as needed.
96
Operation Manual
General Maintenance
Before Starting
6
Tools, spare parts, and supplies
Some of the required tools, spare parts, and supplies are
included in the GC shipping kit, MS shipping kit, or MS tool kit.
You must supply others yourself. Each maintenance procedure
includes a list of the materials required for that procedure.
High voltage precautions
Whenever the MS is plugged in, even if the power switch is off,
potentially dangerous voltage (200/240 VAC) exists on the
wiring and fuses between where the power cord enters the
instrument and the power switch.
When the power switch is on, potentially dangerous voltages
exist on:
• Electronic circuit boards
• Toroidal transformer
• Wires and cables between the boards
• Wires and cables between the boards and the connectors on
the back panel of the MS
• Some connectors on the back panel (for example, the foreline
power receptacle)
Normally, all of these parts are shielded by safety covers. As
long as the safety covers are in place, it should be difficult to
accidentally make contact with dangerous voltages.
WA R N I N G
Perform no maintenance with the MS turned on or plugged into its power source
unless you are instructed to do so by one of the procedures in this chapter.
Some procedures in this chapter require access to the inside of
the MS while the power switch is on. Do not remove any of the
electronics safety covers in any of these procedures. To reduce
the risk of electric shock, follow the procedures carefully.
Dangerous temperatures
Many parts in the MS operate at, or reach, temperatures high
enough to cause serious burns. These parts include, but are not
limited to:
Operation Manual
97
6
General Maintenance
Before Starting
• GC/MS interface
• Analyzer parts
• Vacuum pumps
WA R N I N G
The foreline pump can cause burns if touched when operating.
WA R N I N G
Never touch these parts while your MS is on. After the MS is turned off, give
these parts enough time to cool before handling them.
WA R N I N G
The GC/MS interface heater is powered by a thermal zone on the GC. The
interface heater can be on, and at a dangerously high temperature, even though
the MS is off. The GC/MS interface is well insulated. Even after it is turned off, it
cools very slowly.
The GC inlets and GC oven also operate at very high
temperatures. Use the same caution around these parts. See the
documentation supplied with your GC for more information.
Chemical residue
Only a small portion of your sample is ionized by the ion source.
The majority of any sample passes through the ion source
without being ionized. It is pumped away by the vacuum system.
As a result, the exhaust from the foreline pump will contain
traces of the carrier gas and your samples. Exhaust from the
standard foreline pump also contains tiny droplets of foreline
pump oil.
An oil mist filter is supplied with the standard foreline pump.
This filter stops only pump oil droplets. It does not trap any
other chemicals. If you are using toxic solvents or analyzing
toxic chemicals, install a hose from the mist filter outlet to the
outdoors or into a fume hood vented to the outdoors. Be sure to
comply with your local air quality regulations.
98
Operation Manual
General Maintenance
Before Starting
WA R N I N G
6
The oil trap supplied with the standard foreline pump stops only foreline pump
oil. It does not trap or filter out toxic chemicals. If you are using toxic solvents or
analyzing toxic chemicals, use a hose to vent to a safe location.
The fluids in the foreline pump also collect traces of the samples
being analyzed. All used pump fluid should be considered
hazardous and handled accordingly. Dispose of used fluid as
specified by your local regulations.
WA R N I N G
When replacing pump fluid, use appropriate chemical-resistant gloves and
safety glasses. Avoid all contact with the fluid.
Ion source cleaning
The main effect of operating the MS in CI mode is the need for
more frequent ion source cleaning. In CI operation, the ion
source chamber is subject to more rapid contamination than in
EI operation because of the higher source pressures required
for CI.
WA R N I N G
Always perform any maintenance procedures using hazardous solvents under a
fume hood. Be sure to operate the MS in a well-ventilated room.
Ammonia
Ammonia, used as a reagent gas, increases the need for foreline
pump maintenance. Ammonia causes foreline pump oil to break
down more quickly. Therefore, the oil in the standard foreline
vacuum pump must be checked and replaced more frequently.
Always purge the MS with methane after using ammonia.
Be sure to install the ammonia so the tank is in an upright
position. This will help prevent liquid ammonia from getting
into the flow module.
Operation Manual
99
6
General Maintenance
Maintaining the Vacuum System
Maintaining the Vacuum System
Periodic maintenance
As listed in Table 9, some maintenance tasks for the vacuum
system must be performed periodically. These include:
• Checking the foreline pump fluid color and level (every week)
• Checking the calibration vial(s) (every 6 months)
• Replacing the foreline pump oil and oil mist filter (every 6
months or as needed)
• Replacing the RIS probe seals (yearly or as needed)
Failure to perform these tasks as scheduled can result in
decreased instrument performance. It can also result in damage
to your instrument.
Other procedures
Tasks such as replacing an ion vacuum gauge should be
performed only when needed by a certified Agilent service
personnel. See the Agilent 7200 Accurate-Mass Q-TOF GC/MS
Troubleshooting and Maintenance Manual and see the online
help in the MassHunter WorkStation software for symptoms
that indicate this type of maintenance is required.
More information is available
If you need more information about the locations or functions of
vacuum system components, see the Agilent 7200
Accurate-Mass Q-TOF GC/MS Troubleshooting and Maintenance
Manual.
Most of the procedures in this chapter are illustrated with video
clips on the Agilent GC/MS Hardware User Information &
Instrument Utilities and 7200 Q-TOF GC/MS User Information
disks.
100
Operation Manual
General Maintenance
Maintaining the Analyzer
6
Maintaining the Analyzer
Scheduling
None of the analyzer components requires periodic
maintenance. Some tasks, however, must be performed when
MS behavior indicates they are necessary. These tasks include:
• Cleaning the ion sources
• Replacing filaments
The Agilent 7200 Accurate-Mass Q-TOF GC/MS Troubleshooting
and Maintenance Manual provides information about symptoms
that indicate the need for analyzer maintenance. The
troubleshooting material in the online help in the MassHunter
Workstation software provides more extensive information.
Precautions
Keep components clean during analyzer maintenance. Never
open the analyzer chamber. There are no customer serviceable
parts accessible from this door.
CAUTION
If not done correctly, analyzer maintenance can introduce contaminants into the
MS.
WA R N I N G
The analyzers operate at high temperatures. Do not touch any part until you are
sure it is cool.
Electrostatic discharge
The wires, contacts, and cables connected to the analyzer
components can carry electrostatic discharges (ESDs) to the
electronics boards to which they are connected. This is
especially true of the mass filter (quadrupole) and collision cell
contact wires which can conduct ESD to sensitive components
Operation Manual
101
6
General Maintenance
Maintaining the Analyzer
on the quad driver board. ESD damage may not cause
immediate failure but will gradually degrade performance and
stability.
CAUTION
Electrostatic discharges to analyzer components are conducted to the quad driver
board where they can damage sensitive components. Wear a grounded antistatic
wrist strap and take other antistatic precautions when working on the analyzer.
Analyzer parts that should not be disturbed
The mass filter (quadrupole) and the collision cell require no
periodic maintenance. In general, the mass filter should never
be disturbed. In the event of extreme contamination, it can be
cleaned, but such cleaning should only be done by a trained
Agilent Technologies service representative.
CAUTION
Incorrect handling or cleaning of the mass filter can damage it and have a serious,
negative effect on instrument performance. Never open the analyzer door.
More information is available
If you need more information about the locations or functions of
analyzer components, refer to the Agilent 7200 Accurate-Mass
Q-TOF GC/MS Concepts Guide.
102
Operation Manual
General Maintenance
To Disassemble the EI Ion Source
6
To Disassemble the EI Ion Source


Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)
• Nut driver, 5.5 mm (8710-1220)
• Tweezers (8710-2460)
Procedure
Operation Manual
1
Remove the ion source. See “To Change the Ion Source” on
page 84.
2
Remove the filaments. See “To Remove a Filament” on
page 116.
3
Separate the ion focus and insulator assembly from the
source body. (See Figure 23.)
4
Remove the two screws from the ion focus insulator and
separate it from the ion focus lens.
5
Remove the extractor lens and its insulator from the source
body.
6
Remove the two screws from the RIS bayonet mount on the
bottom of the source body, and remove the RIS bayonet
mount.
7
Remove the repeller assembly from the source body.
8
Disassemble the repeller assembly by separating the
repeller, the repeller cap, ring heater and sensor assembly.
(See Figure 23.)
9
Remove the clocking button from the repeller cap by
removing the screw that holds it in place. (See Figure 23.)
103
6
General Maintenance
To Disassemble the EI Ion Source
Screws
Washers
Bayonet mount
Repeller insulator
Clocking button
Repeller cap
Repeller
Ring heater assembly
RIS Extraction source body
Filaments
Extractor lens insulator
RIS Extraction lens
Ion focus insulator
Ion focus
Screws
Figure 23
104
Disassembling the EI ion source
Operation Manual
General Maintenance
To Assemble the EI Ion Source
6
To Assemble the EI Ion Source


Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)
Procedure
CAUTION
Operation Manual
Always wear clean gloves when working in the analyzer chamber to avoid
contamination.
1
Assemble the repeller assembly, by attaching the repeller to
the repeller cap and connecting the clocking button with the
screw.
2
Align the heater sensor with the source body.
3
Slide the repeller cap onto the heater sensor, and place the
ceramic repeller insulator on top, aligning the screw holes.
4
Place the RIS bayonet mount on top of the ceramic repeller
insulator, and attach with the washers and screws.
5
Attach the extractor lens insulator to the extractor lens,
and slide them onto the other end of the source body
(Figure 23).
6
Place the ion focus insulator on the ion focus lens and
attach with the two screws.
7
Set the ion focus assembly on top of the extractor lens
assembly on the source body.
8
Attach the filaments with the two screws.
105
6
General Maintenance
To Assemble the EI Ion Source
CAUTION
106
While installing, do not overtighten the repeller nut or the ceramic repeller
insulators will break when the source heats up. The nut should only be finger-tight.
Operation Manual
General Maintenance
To Assemble the EI Ion Source
6
Screws
Washers
Bayonet mount
Repeller insulator
Clocking button
Repeller cap
Repeller
Ring heater assembly
RIS Extraction source body
Filaments
Extractor lens insulator
RIS Extraction lens
Ion focus insulator
Ion focus
Screws
Figure 24
Operation Manual
Assembling the EI source
107
6
General Maintenance
To Disassemble the CI Ion Source
To Disassemble the CI Ion Source


Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)
• Nut driver, 5.5 mm (8710-1220)
• Tweezers (8710-2460)
Procedure
108
1
Remove the CI ion source. See “To Change the Ion
Source” on page 84.
2
Remove the filament. See “To Remove a Filament” on
page 116.
3
Remove the ion focus lens and insulator. (See Figure 25.)
4
Remove the two screws from the ion focus lens insulator
and separate it from the ion focus lens.
5
Remove the two screws from the RIS bayonet mount and
remove the repeller assembly.
6
Disassemble the repeller assembly by removing the ceramic
insulator and heater assembly from the repeller. (See
Figure 25.)
7
Take the repeller off the source body.
Operation Manual
General Maintenance
To Disassemble the CI Ion Source
6
Bayonet mount
Clocking button
Ring heater / Sensor assembly
Repeller
RIS CI source body
Filament
Ion focus insulator
Ion focus lens
Figure 25
Operation Manual
Disassembling the CI ion source
109
6
General Maintenance
To Assemble the CI Ion Source
To Assemble the CI Ion Source


Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)
Procedure
CAUTION
CAUTION
Always wear clean gloves when working in the analyzer chamber to avoid
contamination.
1
Place the ceramic heater assembly on top of the repeller,
aligning the grooves on the repeller with the slot on the
heater assembly. (Figure 26).
2
Place the repeller on the source body. (Figure 26).
3
Place the assembled parts into the RIS bayonet mount,
heater side first.
4
Align the interface socket in the source body with the
alignment groove in the RIS bayonet mount. Attach with the
two screws.
5
Place the ion focus and ion focus insulator together and
attach with the two screws.
While installing, do not overtighten the repeller nut or the ceramic repeller insulator
will break when the source heats up. The nut should only be finger-tight.
6
110
Set the filament in place.
Operation Manual
General Maintenance
To Assemble the CI Ion Source
6
7
Place the ion focus assembly on the source body, with the
insulator against the source body. Make sure all pins are
facing in the same direction.
8
Attach with the two screws.
Bayonet mount
Clocking button
Ring heater / Sensor assembly
Repeller
RIS CI source body
Filament
Ion focus insulator
Ion focus lens
Figure 26
Operation Manual
Assembling the CI ion source
111
6
General Maintenance
To Clean the Ion Source
To Clean the Ion Source
Frequency of cleaning
Because the CI ion source operates at much higher pressures
than the EI ion source, it will probably require more frequent
cleaning than the EI ion source. Cleaning of the source is not a
scheduled maintenance procedure. The source should be
cleaned whenever there are performance anomalies that are
associated with a dirty ion source. See the 7200 Q-TOF GC/MS
Troubleshooting and Maintenance Manual for symptoms that
indicate a dirty ion source.
Visual appearance is not an accurate guide to cleanliness of
the CI ion source. The CI ion source can show little or no
discoloration yet still need cleaning. Let analytical
performance be your guide.
Materials needed
• Abrasive paper (5061-5896)
• Alumina abrasive powder (8660-0791)
• Aluminum foil, clean
• Cloths, clean (05980-60051)
• Cotton swabs (5080-5400)
• Glass beakers, 500 mL
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Solvents
• Acetone, reagent grade
• Methanol, reagent grade
• Methylene chloride, reagent grade
• Ultrasonic bath
112
Operation Manual
General Maintenance
To Clean the Ion Source


6
Preparation
1
Disassemble the ion source. See “To Disassemble the EI Ion
Source” on page 103 or “To Disassemble the CI Ion
Source” on page 108.
2
Collect the following parts to be cleaned if you are cleaning
a high sensitivity extractor EI ion source: (Figure 27)
• Repeller
• Source body
• Extractor lens
• Ion focus lens
Collect the following parts to be cleaned if you are cleaning
a CI source:
• Repeller
• Source body
• Ion focus lens
These are the parts that contact the sample or ion beam. The
other parts normally should not require cleaning.
CAUTION
If insulators are dirty, clean them with a cotton swab dampened with reagent-grade
methanol. If that does not clean the insulators, replace them. Do not abrasively or
ultrasonically clean the insulators.
Cleaning the CI ion source is very similar to cleaning the EI ion
source, with the following exceptions:
• The CI ion source may not look dirty but deposits left by
chemical ionization are very difficult to remove. Clean the CI
ion source thoroughly.
• Use a round wooden toothpick to gently clean out the
electron entrance hole in the source body.
• Do not use halogenated solvents. Use hexane for the final
rinse.
CAUTION
Operation Manual
Do not use halogenated solvents to clean the CI ion source.
113
6
General Maintenance
To Clean the Ion Source
Ion focus lens
Figure 27
Extractor lens
Source body
Repeller
CI Source parts to be cleaned
CAUTION
The filaments, source heater assembly, and insulators cannot be cleaned
ultrasonically. Replace these components if major contamination occurs.
3
114
Repeller
Extractor EI Source parts to be cleaned
Ion focus lens
Figure 28
Source body
If the contamination is serious, such as an oil backflow into
the analyzer, seriously consider replacing the contaminated
parts.
Operation Manual
General Maintenance
To Clean the Ion Source
4
6
Abrasively clean the surfaces that contact the sample or ion
beam.
Use an abrasive slurry of alumina powder and
reagent-grade methanol on a cotton swab. Use enough force
to remove all discolorations. Polishing the parts is not
necessary; small scratches will not harm performance. Also
abrasively clean the discolorations where electrons from the
filaments enter the source body.
5
Rinse away all abrasive residue with reagent-grade
methanol.
Make sure all abrasive residue is rinsed away before
ultrasonic cleaning. If the methanol becomes cloudy or
contains visible particles, rinse again.
6
CAUTION
Separate the parts that were abrasively cleaned from the
parts that were not abrasively cleaned.
Always wear clean gloves to prevent contamination when working in the analyzer
chamber.
7
Ultrasonically clean the parts (each group separately) for 15
minutes in each of the following solvents:
• Methylene chloride (reagent-grade)
• Acetone (reagent-grade)
• Methanol (reagent-grade)
WA R N I N G
Operation Manual
All of these solvents are hazardous. Work in a fume hood and take all appropriate
precautions.
8
Place the parts in a clean beaker. Loosely cover the beaker
with clean aluminum foil (dull side down).
9
Dry the cleaned parts in an oven at 100 °C for 5–6 minutes.
115
6
General Maintenance
To Remove a Filament
To Remove a Filament


Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Tweezers (8710-2460)
Procedure
CAUTION
WA R N I N G
116
Always wear clean gloves to prevent contamination when working in the analyzer
chamber.
1
Remove the ion source. See “To Change the Ion Source” on
page 84.
2
Remove the screw holding the filament to the ion source
body. (See Figure 29.)
3
Slide the filament off the ion source assembly. (See
Figure 29.)
The analyzer, GC/MS interface, and other components in the analyzer chamber
operate at very high temperatures. Do not touch any part until you are sure it is
cool.
Operation Manual
General Maintenance
To Remove a Filament
Filaments
Filament
EI Source
Figure 29
6
CI Source
Changing the filament
Operation Manual
117
6
General Maintenance
To Install a Filament
To Install a Filament
Materials needed
• Filament assembly, EI (G7005-60061)
• Filament assembly, CI (G7005-60072)
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Tweezers (8710-2460)
Procedure
CAUTION
118
1
Remove the old filament. (See “To Remove a Filament” on
page 116.)
2
Place the new filament into its position on the ion source
body. (See Figure 29.)
3
Secure the filament to the ion source body with the screw.
4
After installing the filament, verify that it is not grounded
to source body.
5
Reinstall the ion source. (See “To Change the Ion Source” on
page 84.)
6
Autotune the MS.
Do not overtighten the thumbscrew; it can cause air leaks or prevent successful
pumpdown. Do not use a screwdriver to tighten the thumbscrew.
Operation Manual
Agilent Technologies
© Agilent Technologies, Inc.
Printed in USA, August 2014
*G3850-90008*
G3850-90008